From 1a988cfca77c8a26b7de49afa22de9572147dd96 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 1 Oct 2024 00:50:10 +0200 Subject: [PATCH 01/47] Add standard RNA-seq workflows --- ...q-Paired-Mapping-Counting-DEseq2-tests.yml | 57 + .../RNA-seq-Paired-Mapping-Counting-DEseq2.ga | 1298 +++++++++++++++++ 2 files changed, 1355 insertions(+) create mode 100644 workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2-tests.yml create mode 100644 workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2.ga diff --git a/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2-tests.yml b/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2-tests.yml new file mode 100644 index 000000000..8832767df --- /dev/null +++ b/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2-tests.yml @@ -0,0 +1,57 @@ +- doc: Test outline for RNA-seq-Paired-Mapping-Counting-DEseq2 + job: + reference_annotation_gtf: + class: File + location: https://zenodo.org/records/6457007/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz + filetype: gtf + Paired-end FASTQ collection: + class: Collection + collection_type: list:paired + elements: + - class: Collection + type: paired + identifier: GSM461177_untreat_paired + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/6457007/files/GSM461177_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/6457007/files/GSM461177_2.fastqsanger + - class: Collection + type: paired + identifier: GSM461178_untreat_paired + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/6457007/files/GSM461178_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/6457007/files/GSM461178_2.fastqsanger + - class: Collection + type: paired + identifier: GSM461180_treat_paired + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/6457007/files/GSM461180_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/6457007/files/GSM461180_2.fastqsanger + - class: Collection + type: paired + identifier: GSM461181_treat_paired + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/6457007/files/GSM461181_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/6457007/files/GSM461181_2.fastqsanger + reference_genome: dm6full + outputs: + deseq_out: + asserts: + has_line: + line: "FBgn0003360\t2478.41.*\t-3.01.*\t0.11.*\t-25.81.*\t6.0.*4.95.*" + line: "FBgn0052251\t727.62.*\t-0.59.*\t0.15.*\t-3.90.*\t9.34.*\t0.002.*" diff --git a/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2.ga b/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2.ga new file mode 100644 index 000000000..981d4b1e4 --- /dev/null +++ b/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2.ga @@ -0,0 +1,1298 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Reference-based RNA-Seq data analysis", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-5192-126X", + "name": "Pavankumar Videm" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "RNA-seq-Paired-Mapping-Counting-DEseq2", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + 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workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2.ga diff --git a/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2-tests.yml b/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2-tests.yml new file mode 100644 index 000000000..a68fe10df --- /dev/null +++ b/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2-tests.yml @@ -0,0 +1,35 @@ +- doc: Test outline for RNA-seq-Single-Mapping-Counting-DEseq2 + job: + reference_annotation_gtf: + class: File + location: https://zenodo.org/records/6457007/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz + filetype: gtf + Single-end FASTQ collection: + class: Collection + collection_type: list + elements: + - class: File + identifier: GSM461180_treat_paired + location: https://zenodo.org/records/6457007/files/GSM461180_1.fastqsanger + - class: File + identifier: GSM461178_untreat_paired + location: https://zenodo.org/records/6457007/files/GSM461178_1.fastqsanger + - class: File + identifier: GSM461177_untreat_paired + location: https://zenodo.org/records/6457007/files/GSM461177_1.fastqsanger + - class: File + identifier: GSM461182_untreat_single + location: https://zenodo.org/records/6457007/files/GSM461182.fastqsanger + - class: File + identifier: GSM461179_treat_single + location: https://zenodo.org/records/6457007/files/GSM461179.fastqsanger + - class: File + identifier: GSM461176_untreat_single + location: https://zenodo.org/records/6457007/files/GSM461176.fastqsanger + reference_genome: dm6full + outputs: + deseq_out: + asserts: + has_line: + line: "FBgn0003360\t5400.62.*\t-3.19.*\t0.16.*\t-19.00.*\t1.58.*\t7.15.*" + line: "FBgn0052251\t1279.71.*\t-0.40.*\t0.20.*\t-1.93.*\t0.05.*\t0.40.*" diff --git a/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2.ga b/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2.ga new file mode 100644 index 000000000..47390ed12 --- /dev/null +++ b/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2.ga @@ -0,0 +1,1269 @@ +{ + "a_galaxy_workflow": "true", + "annotation": "Reference-based RNA-Seq data analysis", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-5192-126X", + "name": "Pavankumar Videm" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "RNA-seq-Single-Mapping-Counting-DEseq2", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + 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"tool_state": "{\"advanced_options\": {\"esf_cond\": {\"esf\": \"\", \"__current_case__\": 0}, \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}, \"use_beta_priors\": false}, \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"header\": true, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.11.40.8+galaxy0", + "type": "tool", + "uuid": "0e2cccd3-c552-4ebd-b3b4-328893ef9a97", + "when": null, + "workflow_outputs": [ + { + "label": "plots", + "output_name": "plots", + "uuid": "9725f79f-b17a-4143-b446-0b8732f1105b" + }, + { + "label": "deseq_out", + "output_name": "deseq_out", + "uuid": "faa8ad52-94ec-42c6-87d5-b47e9c793210" + } + ] + } + }, + "tags": [ + "transcriptomics" + ], + "uuid": "2e9be2d0-bb73-4404-af74-bc9411d2b1f0", + "version": 1 +} \ No newline at end of file From f9215dc17f179411b371830c0413743af3eabbfe Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 4 Oct 2024 01:21:38 +0200 Subject: [PATCH 03/47] Add QC and DE to the existing RNA-seq PE workflow --- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1361 +++++++++++++---- ...q-Paired-Mapping-Counting-DEseq2-tests.yml | 57 - .../RNA-seq-Paired-Mapping-Counting-DEseq2.ga | 1298 ---------------- ...q-Single-Mapping-Counting-DEseq2-tests.yml | 35 - .../RNA-seq-Single-Mapping-Counting-DEseq2.ga | 1269 --------------- 5 files changed, 1032 insertions(+), 2988 deletions(-) delete mode 100644 workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2-tests.yml delete mode 100644 workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2.ga delete mode 100644 workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2-tests.yml delete mode 100644 workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2.ga diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index ca98e047a..cba76d43a 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,18 +1,25 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.", + "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", "comments": [], "creator": [ { "class": "Person", "identifier": "0000-0002-1964-4960", "name": "Lucille Delisle" + }, + { + "class": "Person", + "identifier": "0000-0002-5192-126X", + "name": "Pavankumar Videm" } ], "format-version": "0.1", "license": "MIT", - "release": "0.9", "name": "RNAseq_PE", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "Should be a list of paired-end RNA-seq fastqs", @@ -23,15 +30,15 @@ "inputs": [ { "description": "Should be a list of paired-end RNA-seq fastqs", - "name": "PE fastq input" + "name": "Collection paired FASTQ files" } ], - "label": "PE fastq input", + "label": "Collection paired FASTQ files", "name": "Input dataset collection", "outputs": [], "position": { "left": 0, - "top": 252.80832516863774 + "top": 420 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -42,218 +49,218 @@ "workflow_outputs": [] }, "1": { - "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "annotation": "Whether to report QC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", - "name": "forward_adapter" + "description": "Whether to report QC", + "name": "Generate QC reports?" } ], - "label": "forward_adapter", + "label": "Generate QC reports?", "name": "Input parameter", "outputs": [], "position": { - "left": 26.45001220703125, - "top": 338.9083312721534 + "left": 40, + "top": 530 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "db025004-00b9-4fa0-b4ae-e47d58a615ae", + "uuid": "f3dcb910-684b-463d-bf98-03bc18451666", "when": null, "workflow_outputs": [] }, "2": { - "annotation": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "annotation": "", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", - "name": "reverse_adapter" + "description": "", + "name": "Reference genome" } ], - "label": "reverse_adapter", + "label": "Reference genome", "name": "Input parameter", "outputs": [], "position": { - "left": 68, - "top": 427.04166257098154 + "left": 70, + "top": 640 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "ad4f5c84-4a83-4d66-afe1-a7fdfc37f638", + "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", "when": null, "workflow_outputs": [] }, "3": { - "annotation": "reference_genome", + "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "reference_genome", - "name": "reference_genome" + "description": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", + "name": "GTF file of annotation" } ], - "label": "reference_genome", - "name": "Input parameter", + "label": "GTF file of annotation", + "name": "Input dataset", "outputs": [], "position": { - "left": 132.63336181640625, - "top": 522.134886401586 + "left": 120, + "top": 740 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", + "type": "data_input", + "uuid": "423b33a8-0778-46a5-b5fb-2a8199660076", "when": null, "workflow_outputs": [] }, "4": { - "annotation": "gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming", + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming", - "name": "gtf" + "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "name": "strandedness" } ], - "label": "gtf", - "name": "Input dataset", + "label": "strandedness", + "name": "Input parameter", "outputs": [], "position": { - "left": 150.60003662109375, - "top": 606.751585620336 + "left": 160, + "top": 830 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\"}", + "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, - "type": "data_input", - "uuid": "423b33a8-0778-46a5-b5fb-2a8199660076", + "type": "parameter_input", + "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", "when": null, "workflow_outputs": [] }, "5": { - "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, "id": 5, "input_connections": {}, "inputs": [ { - "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", - "name": "strandedness" + "description": "Whether FPKM values should be computed with Cufflinks", + "name": "Compute Cufflinks FPKM?" } ], - "label": "strandedness", + "label": "Compute Cufflinks FPKM?", "name": "Input parameter", "outputs": [], "position": { - "left": 181.25, - "top": 667.118284839086 + "left": 190, + "top": 920 }, "tool_id": null, - "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", + "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", "when": null, "workflow_outputs": [] }, "6": { - "annotation": "Whether FPKM values should be computed with cufflinks", + "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "Whether FPKM values should be computed with cufflinks", - "name": "cufflinks_FPKM" + "description": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", + "name": "GTF with regions to exclude from FPKM normalization with Cufflinks" } ], - "label": "cufflinks_FPKM", - "name": "Input parameter", + "label": "GTF with regions to exclude from FPKM normalization with Cufflinks", + "name": "Input dataset", "outputs": [], "position": { - "left": 202.6500244140625, - "top": 735.4800895070166 + "left": 210, + "top": 1020 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", + "type": "data_input", + "uuid": "1d1b3d41-0efa-4ffa-aba9-0e80a51173a5", "when": null, "workflow_outputs": [] }, "7": { - "annotation": "Could be a gtf with for example one entry for the chrM forward and one entry for the chrM reverse", + "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, "id": 7, "input_connections": {}, "inputs": [ { - "description": "Could be a gtf with for example one entry for the chrM forward and one entry for the chrM reverse", - "name": "gtf with regions to exclude from FPKM normalization with Cufflinks" + "description": "Whether FPKM values should be computed with StringTie", + "name": "Compute StringTie FPKM?" } ], - "label": "gtf with regions to exclude from FPKM normalization with Cufflinks", - "name": "Input dataset", + "label": "Compute StringTie FPKM?", + "name": "Input parameter", "outputs": [], "position": { - "left": 226.73333740234375, - "top": 809.5967887257666 + "left": 230, + "top": 1140 }, "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": \"\"}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, - "type": "data_input", - "uuid": "1d1b3d41-0efa-4ffa-aba9-0e80a51173a5", + "type": "parameter_input", + "uuid": "47972cba-6df9-4883-8280-24ea28bcc4bb", "when": null, "workflow_outputs": [] }, "8": { - "annotation": "Whether FPKM values should be computed with StringTie", + "annotation": "Provide experimental and batch details. 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There might be additional columns with one batch information each.", + "name": "Sample table" } ], - "label": "stringtie_FPKM", - "name": "Input parameter", + "label": "Sample table", + "name": "Input dataset", "outputs": [], "position": { - "left": 270.88330078125, - "top": 926.4134391163916 + "left": 260, + "top": 1250 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": null}", "tool_version": null, - "type": "parameter_input", - "uuid": "47972cba-6df9-4883-8280-24ea28bcc4bb", + "type": "data_input", + "uuid": "9b903f17-a37b-48d9-a214-bcdf393a7574", "when": null, "workflow_outputs": [] }, @@ -266,14 +273,6 @@ "library|input_1": { "id": 0, "output_name": "output" - }, - "library|r1|adapters_0|adapter_source|adapter": { - "id": 1, - "output_name": "output" - }, - "library|r2|adapters2_0|adapter_source|adapter": { - "id": 2, - "output_name": "output" } }, "inputs": [ @@ -295,8 +294,8 @@ } ], 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b/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2-tests.yml deleted file mode 100644 index 8832767df..000000000 --- a/workflows/transcriptomics/star-featurecounts-deseq2-pe/RNA-seq-Paired-Mapping-Counting-DEseq2-tests.yml +++ /dev/null @@ -1,57 +0,0 @@ -- doc: Test outline for RNA-seq-Paired-Mapping-Counting-DEseq2 - job: - reference_annotation_gtf: - class: File - location: https://zenodo.org/records/6457007/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz - filetype: gtf - Paired-end FASTQ collection: - class: Collection - collection_type: list:paired - elements: - - class: Collection - type: paired - identifier: GSM461177_untreat_paired - elements: - - class: File - identifier: forward - location: https://zenodo.org/records/6457007/files/GSM461177_1.fastqsanger - - class: File - identifier: reverse - location: https://zenodo.org/records/6457007/files/GSM461177_2.fastqsanger - - class: Collection - type: paired - identifier: GSM461178_untreat_paired - elements: - - class: File - identifier: forward - location: https://zenodo.org/records/6457007/files/GSM461178_1.fastqsanger - - class: File - identifier: reverse - location: https://zenodo.org/records/6457007/files/GSM461178_2.fastqsanger - - class: Collection - type: paired - identifier: GSM461180_treat_paired - elements: - - class: File - identifier: forward - location: https://zenodo.org/records/6457007/files/GSM461180_1.fastqsanger - - class: File - identifier: reverse - location: https://zenodo.org/records/6457007/files/GSM461180_2.fastqsanger - - class: Collection - type: paired - identifier: GSM461181_treat_paired - elements: - - class: File - identifier: forward - location: https://zenodo.org/records/6457007/files/GSM461181_1.fastqsanger - - class: File - identifier: reverse - location: https://zenodo.org/records/6457007/files/GSM461181_2.fastqsanger - reference_genome: dm6full - outputs: - deseq_out: - asserts: - has_line: - line: 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b/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2-tests.yml deleted file mode 100644 index a68fe10df..000000000 --- a/workflows/transcriptomics/star-featurecounts-deseq2-se/RNA-seq-Single-Mapping-Counting-DEseq2-tests.yml +++ /dev/null @@ -1,35 +0,0 @@ -- doc: Test outline for RNA-seq-Single-Mapping-Counting-DEseq2 - job: - reference_annotation_gtf: - class: File - location: https://zenodo.org/records/6457007/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz - filetype: gtf - Single-end FASTQ collection: - class: Collection - collection_type: list - elements: - - class: File - identifier: GSM461180_treat_paired - location: https://zenodo.org/records/6457007/files/GSM461180_1.fastqsanger - - class: File - identifier: GSM461178_untreat_paired - location: https://zenodo.org/records/6457007/files/GSM461178_1.fastqsanger - - class: File - identifier: GSM461177_untreat_paired - location: 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null}", - "tool_version": "2.11.40.8+galaxy0", - "type": "tool", - "uuid": "0e2cccd3-c552-4ebd-b3b4-328893ef9a97", - "when": null, - "workflow_outputs": [ - { - "label": "plots", - "output_name": "plots", - "uuid": "9725f79f-b17a-4143-b446-0b8732f1105b" - }, - { - "label": "deseq_out", - "output_name": "deseq_out", - "uuid": "faa8ad52-94ec-42c6-87d5-b47e9c793210" - } - ] - } - }, - "tags": [ - "transcriptomics" - ], - "uuid": "2e9be2d0-bb73-4404-af74-bc9411d2b1f0", - "version": 1 -} \ No newline at end of file From 626d119f70549ef2a237bb55dcacd96d9c871624 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 4 Oct 2024 02:20:07 +0200 Subject: [PATCH 04/47] update tests.yml --- .../rnaseq-pe/rnaseq-pe-tests.yml | 68 ++++++++++++++----- .../rnaseq-pe/test-data/Sample_table.tabular | 4 ++ 2 files changed, 56 insertions(+), 16 deletions(-) create mode 100644 workflows/transcriptomics/rnaseq-pe/test-data/Sample_table.tabular diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 76be417ce..27a092f9a 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -1,10 +1,14 @@ - doc: Test outline for RNAseq_PE job: - gtf: + GTF file of annotation: class: File - location: https://zenodo.org/record/4541751/files/Drosophila_melanogaster.BDGP6.87.gtf + location: https://zenodo.org/records/13888221/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz filetype: gtf - PE fastq input: + Sample table: + class: File + path: test-data/Sample_table.tabular + filetype: tabular + Collection paired FASTQ files: class: Collection collection_type: list:paired elements: @@ -12,20 +16,47 @@ type: paired identifier: GSM461177 elements: - - identifier: forward - class: File - location: https://zenodo.org/record/4541751/files/GSM461177_1_subsampled.fastqsanger - filetype: fastqsanger - - identifier: reverse - class: File - location: https://zenodo.org/record/4541751/files/GSM461177_2_subsampled.fastqsanger - filetype: fastqsanger - forward_adapter: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC - reverse_adapter: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT - reference_genome: dm6 + - class: File + identifier: forward + location: https://zenodo.org/records/13888221/files/GSM461177_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/13888221/files/GSM461177_2.fastqsanger + - class: Collection + type: paired + identifier: GSM461178 + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/13888221/files/GSM461178_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/13888221/files/GSM461178_2.fastqsanger + - class: Collection + type: paired + identifier: GSM461180 + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/13888221/files/GSM461180_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/13888221/files/GSM461180_2.fastqsanger + - class: Collection + type: paired + identifier: GSM461181 + elements: + - class: File + identifier: forward + location: https://zenodo.org/records/13888221/files/GSM461181_1.fastqsanger + - class: File + identifier: reverse + location: https://zenodo.org/records/13888221/files/GSM461181_2.fastqsanger + Generate QC reports?: true + Reference genome: dm6 strandedness: unstranded - cufflinks_FPKM: false - stringtie_FPKM: true + Compute Cufflinks FPKM?: false + Compute StringTie FPKM?: true outputs: output_log: element_tests: @@ -97,3 +128,8 @@ asserts: has_text: text: "FBgn0031217\tCG11377\tchr2L\t+\t102380\t104142\t1.963814\t33.024075\t62.009155" + deseq_out: + asserts: + has_line: + line: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" + line: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" diff --git a/workflows/transcriptomics/rnaseq-pe/test-data/Sample_table.tabular b/workflows/transcriptomics/rnaseq-pe/test-data/Sample_table.tabular new file mode 100644 index 000000000..053ee24ca --- /dev/null +++ b/workflows/transcriptomics/rnaseq-pe/test-data/Sample_table.tabular @@ -0,0 +1,4 @@ +GSM461181 treat paired +GSM461180 treat paired +GSM461178 untreat paired +GSM461177 untreat paired From b4082f97ff312e8a23780f3b6619569248e95b95 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 4 Oct 2024 20:15:31 +0200 Subject: [PATCH 05/47] update outputs in tests --- .../rnaseq-pe/rnaseq-pe-tests.yml | 52 +++++++++---------- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 18 +++---- 2 files changed, 34 insertions(+), 36 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 27a092f9a..47fb5c50b 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -58,38 +58,36 @@ Compute Cufflinks FPKM?: false Compute StringTie FPKM?: true outputs: - output_log: + multiqc_stats: + asserts: + has_line: + line: "GSM461177\t6.1029\t0.516.*\t0.468.*\t90.67\t0.427.*\t82.73\t0.0409.*\t5.758.*\t14.114.*\t51.0\t35.980.*\t37\t10.0\t1.519.*" + line: "GSM461178\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" + line: "GSM461180\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" + line: "GSM461181\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" + mapped_reads: element_tests: GSM461177: asserts: - - that: "has_text" - text: "Number of input reads |\t1032407" - - that: "has_text" - text: "Uniquely mapped reads number |\t854812" - - that: "has_text" - text: "Number of reads mapped to multiple loci |\t82072" - mapped-reads: - element_tests: - GSM461177: + has_size: + value: 45784586 + delta: 4000000 + GSM461178: asserts: has_size: - value: 89048730 - delta: 8000000 - 'MultiQC on input dataset(s): Stats': - asserts: - has_line: - line: "Sample STAR_mqc_generalstats_star_total_reads_1 STAR_mqc_generalstats_star_mapped_1 STAR_mqc_generalstats_star_mapped_percent_1 STAR_mqc_generalstats_star_uniquely_mapped_1 STAR_mqc_generalstats_star_uniquely_mapped_percent_1 STAR_mqc_generalstats_star_multimapped_1 Cutadapt_mqc_generalstats_cutadapt_percent_trimmed" - has_text_matching: - expression: "GSM461177\t1.0[0-9]*\t0.93[0-9]*\t90.[0-9]*\t0.8[0-9]*\t82.8[0-9]*\t0.08[0-9]*\t6.0[0-9]*" - MultiQC webpage: - asserts: - - that: "has_text" - text: "GSM461177" - - that: "has_text" - text: "Filtered Reads" - - that: "has_text" - text: "STAR" - reads_per_gene from STAR: + value: 47832349 + delta: 4000000 + GSM461180: + asserts: + has_size: + value: 48013469 + delta: 4000000 + GSM461181: + asserts: + has_size: + value: 53466524 + delta: 4000000 + reads_per_gene_from_STAR: element_tests: GSM461177: asserts: diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index cba76d43a..df71bceab 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -5,12 +5,12 @@ "creator": [ { "class": "Person", - "identifier": "0000-0002-1964-4960", + "identifier": "https://orcid.org/0000-0002-1964-4960", "name": "Lucille Delisle" }, { "class": "Person", - "identifier": "0000-0002-5192-126X", + "identifier": "https://orcid.org/0000-0002-5192-126X", "name": "Pavankumar Videm" } ], @@ -2587,15 +2587,15 @@ "uuid": "61638ee7-d466-4b4b-988e-40f898041033", "when": null, "workflow_outputs": [ - { - "label": "plots", - "output_name": "plots", - "uuid": "ac6ab034-3197-4200-ad4c-e859a407247c" - }, { "label": "deseq_out", "output_name": "deseq_out", "uuid": "ba5bd61d-42df-41c1-9424-ece543807248" + }, + { + "label": "plots", + "output_name": "plots", + "uuid": "ac6ab034-3197-4200-ad4c-e859a407247c" } ] } @@ -2603,6 +2603,6 @@ "tags": [ "RNAseq" ], - "uuid": "d1fa2d32-0436-448c-85e6-3087de674917", - "version": 10 + "uuid": "0bb92564-6697-48b3-a4b3-345d107a3cfd", + "version": 1 } \ No newline at end of file From 048f88bcb149659ced661a29e52b32b76d69f7a5 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 7 Oct 2024 12:05:56 +0200 Subject: [PATCH 06/47] add release and correct the asserts --- .../rnaseq-pe/rnaseq-pe-tests.yml | 32 +++++++----- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 49 ++++++++++++------- 2 files changed, 50 insertions(+), 31 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 47fb5c50b..3bc452546 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -91,35 +91,43 @@ element_tests: GSM461177: asserts: - - that: "has_text" - text: "N_ambiguous 25107 5900 5518" - - that: "has_text" - text: "FBgn0010247 13 5 8" + has_text: + text: "N_ambiguous\t15053\t3942\t3628" + text: "FBgn0027948\t252\t118\t135" + GSM461178: + asserts: + has_text: + text: "N_noFeature\t6799\t209643\t209726" + text: "FBgn0027948\t212\t116\t97" HTS count like output: element_tests: - GSM461177: + GSM461180: + asserts: + has_text: + text: "FBgn0027948\t274" + GSM461181: asserts: has_text: - text: "FBgn0010247\t13" + text: "FBgn0027948\t296" both strands coverage: element_tests: GSM461177: asserts: has_size: - value: 9885639 - delta: 900000 + value: 5919847 + delta: 500000 stranded coverage: element_tests: GSM461177_reverse: asserts: has_size: - value: 5920766 - delta: 600000 + value: 3097346 + delta: 300000 GSM461177_forward: asserts: has_size: - value: 5920766 - delta: 600000 + value: 3093571 + delta: 300000 genes_expression_stringtie: element_tests: GSM461177: diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index df71bceab..eda8f9c18 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -16,6 +16,7 @@ ], "format-version": "0.1", "license": "MIT", + "release": "0.10", "name": "RNAseq_PE", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -2279,22 +2280,27 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "b5e9c0d2-62f4-41b2-a1c7-5677d8555fd4", "when": null, "workflow_outputs": [ { - "label": "html_report", + "label": "multiqc_stats", + "output_name": "stats", + "uuid": "cb34b85e-c36d-4dd3-8b29-640faa8357c6" + }, + { + "label": "multiqc_html_report", "output_name": "html_report", - "uuid": "fc0a8ca4-556e-4889-aac0-dba7934a3e75" + "uuid": "ba992ca2-42f2-4827-8a8c-0c8a756aeeb7" } ] } }, "tags": [], - "uuid": "5cba6b7d-fcb0-4f2f-a660-4b4484706a2a" + "uuid": "4462d9b6-c5cf-481a-b184-5a5e5466b488" }, "tool_id": null, "type": "subworkflow", @@ -2302,9 +2308,14 @@ "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "qc_html_report", - "output_name": "html_report", - "uuid": "2c18a720-6327-4538-b2a8-cdd19594ee9a" + "label": "multiqc_stats", + "output_name": "multiqc_stats", + "uuid": "041c8433-ab5c-44bb-ac1b-eca2bf48fa94" + }, + { + "label": "multiqc_html_report", + "output_name": "multiqc_html_report", + "uuid": "6cb02d1e-f8fa-480a-b019-edc686755d6e" } ] }, @@ -2411,15 +2422,15 @@ "uuid": "c38c3093-61e6-49f9-b756-8e25c37c8c68", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "genes_expression_cufflinks", - "output_name": "genes_expression", - "uuid": "807a3d5e-8f42-43c2-a627-a4500c721939" - }, { "label": "transcripts_expression_cufflinks", "output_name": "transcripts_expression", "uuid": "bb2b3707-a64b-4fd6-801e-9d2ff1e3dbda" + }, + { + "label": "genes_expression_cufflinks", + "output_name": "genes_expression", + "uuid": "807a3d5e-8f42-43c2-a627-a4500c721939" } ] }, @@ -2587,15 +2598,15 @@ "uuid": "61638ee7-d466-4b4b-988e-40f898041033", "when": null, "workflow_outputs": [ - { - "label": "deseq_out", - "output_name": "deseq_out", - "uuid": "ba5bd61d-42df-41c1-9424-ece543807248" - }, { "label": "plots", "output_name": "plots", "uuid": "ac6ab034-3197-4200-ad4c-e859a407247c" + }, + { + "label": "deseq_out", + "output_name": "deseq_out", + "uuid": "ba5bd61d-42df-41c1-9424-ece543807248" } ] } @@ -2603,6 +2614,6 @@ "tags": [ "RNAseq" ], - "uuid": "0bb92564-6697-48b3-a4b3-345d107a3cfd", - "version": 1 + "uuid": "4512dec1-5796-4f12-b906-bc616f66b1cb", + "version": 3 } \ No newline at end of file From dd1a9d869cc2db53be727bad9fe240fac10cb5e9 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 9 Oct 2024 14:05:33 +0200 Subject: [PATCH 07/47] update changelog and tests --- .../transcriptomics/rnaseq-pe/CHANGELOG.md | 7 +++++++ .../rnaseq-pe/rnaseq-pe-tests.yml | 18 +++++++++--------- 2 files changed, 16 insertions(+), 9 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 64d12ef64..1f1bec2eb 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -1,5 +1,12 @@ # Changelog +## [0.10] 2024-09-23 + +### Manual update +- Using a new subsampled test data from Zenodo record https://zenodo.org/records/13888221 +- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, Picard reports +- Added DESeq2 step that uses tags to choose factors + ## [0.9] 2024-09-23 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 3bc452546..8c6102827 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -60,11 +60,11 @@ outputs: multiqc_stats: asserts: - has_line: - line: "GSM461177\t6.1029\t0.516.*\t0.468.*\t90.67\t0.427.*\t82.73\t0.0409.*\t5.758.*\t14.114.*\t51.0\t35.980.*\t37\t10.0\t1.519.*" - line: "GSM461178\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" - line: "GSM461180\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" - line: "GSM461181\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" + has_text_matching: + expression: "GSM461177\t6.1029\t0.516.*\t0.468.*\t90.67\t0.427.*\t82.73\t0.0409.*\t5.758.*\t14.114.*\t51.0\t35.980.*\t37\t10.0\t1.519.*" + expression: "GSM461178\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" + expression: "GSM461180\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" + expression: "GSM461181\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" mapped_reads: element_tests: GSM461177: @@ -133,9 +133,9 @@ GSM461177: asserts: has_text: - text: "FBgn0031217\tCG11377\tchr2L\t+\t102380\t104142\t1.963814\t33.024075\t62.009155" + text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" deseq_out: asserts: - has_line: - line: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" - line: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" + has_text: + text: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" + text: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" From 721799bfd636efaf49bba57f35bde61c191926cf Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 9 Oct 2024 17:02:14 +0200 Subject: [PATCH 08/47] fix asserts --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 8c6102827..1fcad2809 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -136,6 +136,6 @@ text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" deseq_out: asserts: - has_text: - text: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" - text: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" + has_text_matching: + expression: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" + expression: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" From 52dfef58d3f84bf1acb27d2605e7b556af4f8a2e Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 9 Oct 2024 17:49:52 +0200 Subject: [PATCH 09/47] use the old gtf file link --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 1fcad2809..efcb3765f 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -2,7 +2,7 @@ job: GTF file of annotation: class: File - location: https://zenodo.org/records/13888221/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz + location: https://zenodo.org/record/4541751/files/Drosophila_melanogaster.BDGP6.87.gtf filetype: gtf Sample table: class: File From 38df98c0d77f316c8d754ef6255f1c88fc89af50 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 11 Oct 2024 02:00:26 +0200 Subject: [PATCH 10/47] update tests --- .../rnaseq-pe/rnaseq-pe-tests.yml | 45 +++++++-------- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 55 ++++++++++++++++--- 2 files changed, 71 insertions(+), 29 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index efcb3765f..1675e3033 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -56,6 +56,7 @@ Reference genome: dm6 strandedness: unstranded Compute Cufflinks FPKM?: false + GTF with regions to exclude from FPKM normalization with Cufflinks: null Compute StringTie FPKM?: true outputs: multiqc_stats: @@ -65,6 +66,11 @@ expression: "GSM461178\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" expression: "GSM461180\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" expression: "GSM461181\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" + deseq_out: + asserts: + has_text_matching: + expression: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" + expression: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" mapped_reads: element_tests: GSM461177: @@ -99,23 +105,6 @@ has_text: text: "N_noFeature\t6799\t209643\t209726" text: "FBgn0027948\t212\t116\t97" - HTS count like output: - element_tests: - GSM461180: - asserts: - has_text: - text: "FBgn0027948\t274" - GSM461181: - asserts: - has_text: - text: "FBgn0027948\t296" - both strands coverage: - element_tests: - GSM461177: - asserts: - has_size: - value: 5919847 - delta: 500000 stranded coverage: element_tests: GSM461177_reverse: @@ -128,14 +117,26 @@ has_size: value: 3093571 delta: 300000 + HTS count like output: + element_tests: + GSM461180: + asserts: + has_text: + text: "FBgn0027948\t274" + GSM461181: + asserts: + has_text: + text: "FBgn0027948\t296" genes_expression_stringtie: element_tests: GSM461177: asserts: has_text: text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" - deseq_out: - asserts: - has_text_matching: - expression: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" - expression: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" + both strands coverage: + element_tests: + GSM461177: + asserts: + has_size: + value: 5919847 + delta: 500000 diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index eda8f9c18..e88343c13 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -74,7 +74,13 @@ "type": "parameter_input", "uuid": "f3dcb910-684b-463d-bf98-03bc18451666", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "8d3db64d-ec67-4032-883b-61a8de87ac7b" + } + ] }, "2": { "annotation": "", @@ -101,7 +107,13 @@ "type": "parameter_input", "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d4ee9258-46bb-49c0-88bc-39d2189956aa" + } + ] }, "3": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", @@ -155,7 +167,13 @@ "type": "parameter_input", "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c954dcb9-3434-4150-a07d-0bda05c22631" + } + ] }, "5": { "annotation": "Whether FPKM values should be computed with Cufflinks", @@ -182,7 +200,13 @@ "type": "parameter_input", "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "6354fbf6-e128-4408-8730-5c1737d60a48" + } + ] }, "6": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -209,7 +233,13 @@ "type": "data_input", "uuid": "1d1b3d41-0efa-4ffa-aba9-0e80a51173a5", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "2e666267-a4c6-4936-9ae2-397e93a81093" + } + ] }, "7": { "annotation": "Whether FPKM values should be computed with StringTie", @@ -236,7 +266,13 @@ "type": "parameter_input", "uuid": "47972cba-6df9-4883-8280-24ea28bcc4bb", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f7ce7395-f514-410f-b59c-cb7289153b40" + } + ] }, "8": { "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", @@ -1617,6 +1653,11 @@ "uuid": "d16e1013-cc55-4143-90a4-d58b24684f68", "when": null, "workflow_outputs": [ + { + "label": null, + "output_name": "0:output", + "uuid": "b0cee4ec-7486-4b9e-929c-f94f3149551b" + }, { "label": "stranded coverage", "output_name": "stranded coverage", @@ -2616,4 +2657,4 @@ ], "uuid": "4512dec1-5796-4f12-b906-bc616f66b1cb", "version": 3 -} \ No newline at end of file +} From 7a238a8a2f8ee5a8e63d8b4a36cb02582328fcdc Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 11 Oct 2024 17:52:13 +0200 Subject: [PATCH 11/47] add alternative featurecounts output --- .../rnaseq-pe/rnaseq-pe-tests.yml | 63 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1391 +++++++++++------ 2 files changed, 964 insertions(+), 490 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 1675e3033..cdc4f1adb 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -52,25 +52,27 @@ - class: File identifier: reverse location: https://zenodo.org/records/13888221/files/GSM461181_2.fastqsanger - Generate QC reports?: true - Reference genome: dm6 + Use featureCounts for generating count tables: true strandedness: unstranded Compute Cufflinks FPKM?: false GTF with regions to exclude from FPKM normalization with Cufflinks: null Compute StringTie FPKM?: true + DEseq2 batch factors: null + Generate QC reports?: true + Reference genome: dm6 outputs: - multiqc_stats: - asserts: - has_text_matching: - expression: "GSM461177\t6.1029\t0.516.*\t0.468.*\t90.67\t0.427.*\t82.73\t0.0409.*\t5.758.*\t14.114.*\t51.0\t35.980.*\t37\t10.0\t1.519.*" - expression: "GSM461178\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" - expression: "GSM461180\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" - expression: "GSM461181\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" deseq_out: asserts: has_text_matching: expression: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" expression: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" + multiqc_stats: + asserts: + has_text_matching: + expression: "GSM461177\t0.406.*\t53.516.*\t6.1029\t0.516.*\t0.468.*\t90.67\t0.427.*\t82.73\t0.0409.*\t5.758.*\t14.114.*\t51.0\t35.980.*\t37\t10.0\t1.519.*" + expression: "GSM461178\t0.403.*\t57.242.*\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" + expression: "GSM461180\t0.3917.*\t55.727.*\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" + expression: "GSM461181\t0.501.*\t58.451.*\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" mapped_reads: element_tests: GSM461177: @@ -93,46 +95,16 @@ has_size: value: 53466524 delta: 4000000 - reads_per_gene_from_STAR: - element_tests: - GSM461177: - asserts: - has_text: - text: "N_ambiguous\t15053\t3942\t3628" - text: "FBgn0027948\t252\t118\t135" - GSM461178: - asserts: - has_text: - text: "N_noFeature\t6799\t209643\t209726" - text: "FBgn0027948\t212\t116\t97" - stranded coverage: - element_tests: - GSM461177_reverse: - asserts: - has_size: - value: 3097346 - delta: 300000 - GSM461177_forward: - asserts: - has_size: - value: 3093571 - delta: 300000 - HTS count like output: + counts_table: element_tests: GSM461180: asserts: has_text: - text: "FBgn0027948\t274" + text: "FBgn0027948\t276" GSM461181: asserts: has_text: - text: "FBgn0027948\t296" - genes_expression_stringtie: - element_tests: - GSM461177: - asserts: - has_text: - text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" + text: "FBgn0027948\t297" both strands coverage: element_tests: GSM461177: @@ -140,3 +112,10 @@ has_size: value: 5919847 delta: 500000 + genes_expression_stringtie: + element_tests: + GSM461177: + asserts: + has_text: + text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" + diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index e88343c13..a0fe1fc5c 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,7 +1,56 @@ { "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", - "comments": [], + "comments": [ + { + "child_steps": [ + 22, + 27, + 28, + 21, + 18, + 6, + 30, + 19 + ], + "color": "turquoise", + "data": { + "title": "Count table processing" + }, + "id": 0, + "position": [ + 1001.6, + 838.5059588256875 + ], + "size": [ + 1268, + 696 + ], + "type": "frame" + }, + { + "child_steps": [ + 14, + 17, + 15, + 16 + ], + "color": "lime", + "data": { + "title": "Map Strandedness parameter" + }, + "id": 1, + "position": [ + 620.6, + 1208.9059588256873 + ], + "size": [ + 252.5, + 728.6 + ], + "type": "frame" + } + ], "creator": [ { "class": "Person", @@ -39,7 +88,7 @@ "outputs": [], "position": { "left": 0, - "top": 420 + "top": 830.1582083386254 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -66,7 +115,7 @@ "outputs": [], "position": { "left": 40, - "top": 530 + "top": 940.1582083386254 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -78,19 +127,19 @@ { "label": null, "output_name": "output", - "uuid": "8d3db64d-ec67-4032-883b-61a8de87ac7b" + "uuid": "1372534a-be71-42ce-ad50-d900dc68f003" } ] }, "2": { - "annotation": "", + "annotation": "Select the reference genome", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Select the reference genome", "name": "Reference genome" } ], @@ -98,8 +147,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 70, - "top": 640 + "left": 69.99997051198416, + "top": 1051.7939115602285 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -111,7 +160,7 @@ { "label": null, "output_name": "output", - "uuid": "d4ee9258-46bb-49c0-88bc-39d2189956aa" + "uuid": "992bc1f7-451d-4d32-b1f2-b579e2a39ff7" } ] }, @@ -131,8 +180,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 120, - "top": 740 + "left": 119.99999475982484, + "top": 1148.9657432902018 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -143,11 +192,44 @@ "workflow_outputs": [] }, "4": { - "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "annotation": "Use featureCounts tool instead of RNA STAR?", "content_id": null, "errors": null, "id": 4, "input_connections": {}, + "inputs": [ + { + "description": "Use featureCounts tool instead of RNA STAR?", + "name": "Use featureCounts for generating count tables" + } + ], + "label": "Use featureCounts for generating count tables", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 159.66015029117847, + "top": 1257.6991448141564 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "8775ddf1-48f2-423e-813a-b5d302888580", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f7e80449-225d-40de-9aae-588d50c21521" + } + ] + }, + "5": { + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, "inputs": [ { "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -158,8 +240,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 160, - "top": 830 + "left": 203.2055169930919, + "top": 1393.3511175991457 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -171,15 +253,49 @@ { "label": null, "output_name": "output", - "uuid": "c954dcb9-3434-4150-a07d-0bda05c22631" + "uuid": "4028c62d-e184-43dd-92d5-d46c61789e67" } ] }, - "5": { + "6": { + "annotation": "This file will be used in MultiQC if the user opts out of featureCounts to generate count files. ", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [], + "label": "A dummy featureCounts summary file", + "name": "Create text file", + "outputs": [ + { + "name": "outfile", + "type": "txt" + } + ], + "position": { + "left": 1021.6168910011272, + "top": 981.0332028479149 + }, + "post_job_actions": {}, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", + "tool_shed_repository": { + "changeset_revision": "86755160afbf", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": \"Status\\tFeaturecounts_was_not_used\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}, {\"__index__\": 1, \"line\": \"Assigned\\t0\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}, {\"__index__\": 2, \"line\": \"Unassigned_Unmapped\\t0\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "9.3+galaxy1", + "type": "tool", + "uuid": "be0268be-a3ec-4d75-854b-d8eecf4b4521", + "when": null, + "workflow_outputs": [] + }, + "7": { "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, - "id": 5, + "id": 7, "input_connections": {}, "inputs": [ { @@ -191,8 +307,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 190, - "top": 920 + "left": 228.09439688484417, + "top": 1488.490577464827 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -204,15 +320,15 @@ { "label": null, "output_name": "output", - "uuid": "6354fbf6-e128-4408-8730-5c1737d60a48" + "uuid": "635458e7-d351-4fae-b9df-12f1b1d344f6" } ] }, - "6": { + "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 6, + "id": 8, "input_connections": {}, "inputs": [ { @@ -224,8 +340,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 210, - "top": 1020 + "left": 259.4363655681731, + "top": 1606.778737326356 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -237,15 +353,15 @@ { "label": null, "output_name": "output", - "uuid": "2e666267-a4c6-4936-9ae2-397e93a81093" + "uuid": "bb798e6d-6a99-4402-a769-cca1db62d630" } ] }, - "7": { + "9": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 7, + "id": 9, "input_connections": {}, "inputs": [ { @@ -257,8 +373,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 230, - "top": 1140 + "left": 268.103514973962, + "top": 1727.9661626467607 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -270,15 +386,15 @@ { "label": null, "output_name": "output", - "uuid": "f7ce7395-f514-410f-b59c-cb7289153b40" + "uuid": "8660bcf9-5076-445f-897a-ad1939a2879f" } ] }, - "8": { + "10": { "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", "content_id": null, "errors": null, - "id": 8, + "id": 10, "input_connections": {}, "inputs": [ { @@ -290,22 +406,55 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 260, - "top": 1250 + "left": 271.9528882100886, + "top": 1822.7289738185475 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": null}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", "tool_version": null, "type": "data_input", "uuid": "9b903f17-a37b-48d9-a214-bcdf393a7574", "when": null, "workflow_outputs": [] }, - "9": { + "11": { + "annotation": "Tabular file with additional batch factors to include in the model", + "content_id": null, + "errors": null, + "id": 11, + "input_connections": {}, + "inputs": [ + { + "description": "Tabular file with additional batch factors to include in the model", + "name": "DEseq2 batch factors" + } + ], + "label": "DEseq2 batch factors", + "name": 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"type": "tabular" - }, - { - "name": "assembled_isoforms", - "type": "gtf" }, { - "name": "total_map_mass", - "type": "txt" - }, - { - "name": "skipped", - "type": "gtf" - } - ], - "position": { - "left": 1400, - "top": 1160 - }, - "post_job_actions": { - "HideDatasetActionassembled_isoforms": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "assembled_isoforms" - }, - "HideDatasetActionskipped": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "skipped" - }, - "HideDatasetActiontotal_map_mass": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "total_map_mass" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", - "tool_shed_repository": { - "changeset_revision": "d080005cffe1", - "name": "cufflinks", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, 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\"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.3+galaxy0", - "type": "tool", - "uuid": "0403b248-c73c-4a1b-85fd-64f36278c952", - "when": "$(inputs.when)", - "workflow_outputs": [ - { - "label": "genes_expression_stringtie", - "output_name": "gene_abundance_estimation", - "uuid": "fc2a77c2-1868-46c0-ad76-648484d764a2" + "label": "multiqc_stats", + "output_name": "multiqc_stats", + "uuid": "041c8433-ab5c-44bb-ac1b-eca2bf48fa94" } ] }, - "22": { + "30": { "annotation": "", "content_id": "__TAG_FROM_FILE__", "errors": null, - "id": 22, + "id": 30, "input_connections": { "input": { - "id": 18, - "output_name": "outfile" + "id": 28, + "output_name": "data_param" }, "tags": { - "id": 14, + "id": 19, "output_name": "outfile" } }, @@ -2576,8 +3052,8 @@ } ], "position": { - "left": 2020, - "top": 910 + "left": 2041.3664627675912, + "top": 1244.3438104243314 }, "post_job_actions": {}, "tool_id": "__TAG_FROM_FILE__", @@ -2588,22 +3064,26 @@ "when": null, "workflow_outputs": [] }, - "23": { - "annotation": "", + "31": { + "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0", "errors": null, - "id": 23, + "id": 31, "input_connections": { + "batch_factors": { + "id": 11, + "output_name": "output" + }, + "header": { + "id": 4, + "output_name": "output" + }, "select_data|countsFile": { - "id": 22, + "id": 30, "output_name": "output" } }, "inputs": [ - { - "description": "runtime parameter for tool DESeq2", - "name": "batch_factors" - }, { "description": "runtime parameter for tool DESeq2", "name": "select_data" @@ -2622,10 +3102,25 @@ } ], "position": { - "left": 2390, - "top": 880 + "left": 2385.207822325581, + "top": 904.4145593557384 + }, + "post_job_actions": { + "RenameDatasetActiondeseq_out": { + "action_arguments": { + "newname": "Differential expression analysis using DESeq2" + }, + "action_type": "RenameDatasetAction", + "output_name": "deseq_out" + }, + "RenameDatasetActionplots": { + "action_arguments": { + "newname": "DESeq2 plots" + }, + "action_type": "RenameDatasetAction", + "output_name": "plots" + } }, - "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0", "tool_shed_repository": { "changeset_revision": "9a882d108833", @@ -2633,21 +3128,21 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"esf_cond\": {\"esf\": \"\", \"__current_case__\": 0}, \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}, \"use_beta_priors\": false}, \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"header\": true, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"esf_cond\": {\"esf\": \"\", \"__current_case__\": 0}, \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}, \"use_beta_priors\": false}, \"batch_factors\": {\"__class__\": \"ConnectedValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.11.40.8+galaxy0", "type": "tool", "uuid": "61638ee7-d466-4b4b-988e-40f898041033", "when": null, "workflow_outputs": [ { - "label": "plots", - "output_name": "plots", - "uuid": "ac6ab034-3197-4200-ad4c-e859a407247c" + "label": "deseq2_out", + "output_name": "deseq_out", + "uuid": "f2d85a14-6e83-4cbf-a34c-39b276e08acd" }, { - "label": "deseq_out", - "output_name": "deseq_out", - "uuid": "ba5bd61d-42df-41c1-9424-ece543807248" + "label": "deseq2_plots", + "output_name": "plots", + "uuid": "318d01c1-ee47-4ba9-8474-f2e0f7e91b42" } ] } @@ -2655,6 +3150,6 @@ "tags": [ "RNAseq" ], - "uuid": "4512dec1-5796-4f12-b906-bc616f66b1cb", - "version": 3 + "uuid": "e37ed9c9-1523-46cd-b64d-95cee39402f0", + "version": 24 } From 31839d1b97f09dbb10de1346df9e77f9e4aeaa8f Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 11 Oct 2024 17:59:56 +0200 Subject: [PATCH 12/47] correct the output name --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index cdc4f1adb..8b6a1d651 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -61,7 +61,7 @@ Generate QC reports?: true Reference genome: dm6 outputs: - deseq_out: + deseq2_out: asserts: has_text_matching: expression: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" From 73eb051d95b57626c01e51587418b1f66f24ff71 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 15 Oct 2024 15:14:34 +0200 Subject: [PATCH 13/47] add uniq names to collections to fix merging --- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 23 +++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index a0fe1fc5c..9bbf8315d 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1477,6 +1477,9 @@ "format-version": "0.1", "license": "MIT", "name": "Re-arrange Stranded RNA-seq coverage", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -1858,7 +1861,13 @@ "type": "tool", "uuid": "e9dcd2df-2834-4e9a-bef2-7666de012b8a", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "Relabelled strand 1", + "output_name": "output", + "uuid": "53fcc658-d461-4cf2-8c6b-2bdb89159fee" + } + ] }, "9": { "annotation": "", @@ -1906,7 +1915,13 @@ "type": "tool", "uuid": "147ccbb0-b951-4851-9bf5-2c6b439ac1b6", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": "Relabelled strand 2", + "output_name": "output", + "uuid": "8ea49a28-635e-40c0-97d1-a8360f8347bf" + } + ] }, "10": { "annotation": "", @@ -3150,6 +3165,6 @@ "tags": [ "RNAseq" ], - "uuid": "e37ed9c9-1523-46cd-b64d-95cee39402f0", - "version": 24 + "uuid": "3855595a-2271-4c5a-b4dc-820a10fd3fd4", + "version": 26 } From f3aaa512602b5040140abff6d0cc28c1cd46ea34 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 15 Oct 2024 16:44:56 +0200 Subject: [PATCH 14/47] retry --- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 234 +++++++----------- 1 file changed, 84 insertions(+), 150 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 9bbf8315d..1d5501254 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -2,6 +2,28 @@ "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", "comments": [ + { + "child_steps": [ + 14, + 15, + 16, + 17 + ], + "color": "lime", + "data": { + "title": "Map Strandedness parameter" + }, + "id": 1, + "position": [ + 620.6, + 1208.9059588256873 + ], + "size": [ + 252.5, + 728.6 + ], + "type": "frame" + }, { "child_steps": [ 22, @@ -27,28 +49,6 @@ 696 ], "type": "frame" - }, - { - "child_steps": [ - 14, - 17, - 15, - 16 - ], - "color": "lime", - "data": { - "title": "Map Strandedness parameter" - }, - "id": 1, - "position": [ - 620.6, - 1208.9059588256873 - ], - "size": [ - 252.5, - 728.6 - ], - "type": "frame" } ], "creator": [ @@ -123,13 +123,7 @@ "type": "parameter_input", "uuid": "f3dcb910-684b-463d-bf98-03bc18451666", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "1372534a-be71-42ce-ad50-d900dc68f003" - } - ] + "workflow_outputs": [] }, "2": { "annotation": "Select the reference genome", @@ -156,13 +150,7 @@ "type": "parameter_input", "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "992bc1f7-451d-4d32-b1f2-b579e2a39ff7" - } - ] + "workflow_outputs": [] }, "3": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", @@ -216,13 +204,7 @@ "type": "parameter_input", "uuid": "8775ddf1-48f2-423e-813a-b5d302888580", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "f7e80449-225d-40de-9aae-588d50c21521" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -249,13 +231,7 @@ "type": "parameter_input", "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "4028c62d-e184-43dd-92d5-d46c61789e67" - } - ] + "workflow_outputs": [] }, "6": { "annotation": "This file will be used in MultiQC if the user opts out of featureCounts to generate count files. ", @@ -316,13 +292,7 @@ "type": "parameter_input", "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "635458e7-d351-4fae-b9df-12f1b1d344f6" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -349,13 +319,7 @@ "type": "data_input", "uuid": "1d1b3d41-0efa-4ffa-aba9-0e80a51173a5", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "bb798e6d-6a99-4402-a769-cca1db62d630" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "Whether FPKM values should be computed with StringTie", @@ -382,13 +346,7 @@ "type": "parameter_input", "uuid": "47972cba-6df9-4883-8280-24ea28bcc4bb", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "8660bcf9-5076-445f-897a-ad1939a2879f" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", @@ -442,13 +400,7 @@ "type": "data_input", "uuid": "96d02185-64bb-4d77-b986-cc6209329334", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e474fa6b-c539-49a9-887e-e441a68db198" - } - ] + "workflow_outputs": [] }, "12": { "annotation": "", @@ -1100,7 +1052,7 @@ "outputs": [], "position": { "left": 2355.1045110079544, - "top": 0.0 + "top": 0 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1498,7 +1450,7 @@ "outputs": [], "position": { "left": 0, - "top": 86.19999694824209 + "top": 370 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -1506,23 +1458,17 @@ "type": "parameter_input", "uuid": "56955f25-7e9e-4201-a056-b61f47359c84", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2d815f2b-a706-43a8-a317-7dc434c6fea8" - } - ] + "workflow_outputs": [] }, "1": { - "annotation": "", + "annotation": "From STAR strand 1", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "", + "description": "From STAR strand 1", "name": "Bedgraph strand 1" } ], @@ -1530,8 +1476,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 62.75, - "top": 182.01666259765614 + "left": 0, + "top": 472 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bedgraph\"], \"tag\": null, \"collection_type\": \"list\"}", @@ -1557,8 +1503,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 124.7500000000002, - "top": 291.0166625976562 + "left": 569.999952609169, + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"bedgraph\"], \"tag\": null, \"collection_type\": \"list\"}", @@ -1585,7 +1531,7 @@ "name": "input_param_type" } ], - "label": "Get replacement for strand1", + "label": "Get replacement for strand2", "name": "Map parameter value", "outputs": [ { @@ -1594,8 +1540,8 @@ } ], "position": { - "left": 445, - "top": 105 + "left": 289.9999763045845, + "top": 51 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -1616,10 +1562,10 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_forward\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_reverse\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_forward\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_reverse\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_forward\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_reverse\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "b7e2cedf-e846-4553-9e48-4aa9a93d40b2", + "uuid": "2ec50fce-ef76-4f56-9fc6-5c6b34c6593e", "when": null, "workflow_outputs": [] }, @@ -1640,7 +1586,7 @@ "name": "input_param_type" } ], - "label": "Get replacement for strand2", + "label": "Get replacement for strand1", "name": "Map parameter value", "outputs": [ { @@ -1649,8 +1595,8 @@ } ], "position": { - "left": 491, - "top": 283 + "left": 289.9999763045845, + "top": 359 }, "post_job_actions": { "HideDatasetActionoutput_param_boolean": { @@ -1671,10 +1617,10 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_reverse\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_forward\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_reverse\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"$1_forward\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"$1_reverse\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"$1_forward\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "2ec50fce-ef76-4f56-9fc6-5c6b34c6593e", + "uuid": "b7e2cedf-e846-4553-9e48-4aa9a93d40b2", "when": null, "workflow_outputs": [] }, @@ -1699,8 +1645,8 @@ } ], "position": { - "left": 351.00000000000017, - "top": 0 + "left": 289.9999763045845, + "top": 225 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2", @@ -1733,7 +1679,7 @@ } }, "inputs": [], - "label": "New labels strand 1", + "label": "New labels strand 2", "name": "Replace", "outputs": [ { @@ -1742,8 +1688,8 @@ } ], "position": { - "left": 782, - "top": 76 + "left": 569.999952609169, + "top": 123 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1762,7 +1708,7 @@ "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"^(.+)$\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "9.3+galaxy1", "type": "tool", - "uuid": "4eb0d67c-f53c-4f84-90fc-3db41e4f0aa7", + "uuid": "ec10a98b-adb9-4037-9137-1717068d7157", "when": null, "workflow_outputs": [] }, @@ -1782,7 +1728,7 @@ } }, "inputs": [], - "label": "New labels strand 2", + "label": "New labels strand 1", "name": "Replace", "outputs": [ { @@ -1791,8 +1737,8 @@ } ], "position": { - "left": 821, - "top": 276 + "left": 569.999952609169, + "top": 328 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1811,7 +1757,7 @@ "tool_state": "{\"find_and_replace\": [{\"__index__\": 0, \"find_pattern\": \"^(.+)$\", \"replace_pattern\": {\"__class__\": \"ConnectedValue\"}, \"is_regex\": true, \"global\": true, \"caseinsensitive\": false, \"wholewords\": false, \"skip_first_line\": false, \"searchwhere\": {\"searchwhere_select\": \"line\", \"__current_case__\": 0}}], \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "9.3+galaxy1", "type": "tool", - "uuid": "ec10a98b-adb9-4037-9137-1717068d7157", + "uuid": "4eb0d67c-f53c-4f84-90fc-3db41e4f0aa7", "when": null, "workflow_outputs": [] }, @@ -1826,7 +1772,7 @@ "output_name": "outfile" }, "input": { - "id": 1, + "id": 2, "output_name": "output" } }, @@ -1836,7 +1782,7 @@ "name": "how" } ], - "label": "Relabelled strand 1", + "label": "Relabelled strand 2", "name": "Relabel identifiers", "outputs": [ { @@ -1845,8 +1791,8 @@ } ], "position": { - "left": 1056, - "top": 176.99999999999994 + "left": 849.9998437853558, + "top": 106 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1859,15 +1805,9 @@ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "e9dcd2df-2834-4e9a-bef2-7666de012b8a", + "uuid": "147ccbb0-b951-4851-9bf5-2c6b439ac1b6", "when": null, - "workflow_outputs": [ - { - "label": "Relabelled strand 1", - "output_name": "output", - "uuid": "53fcc658-d461-4cf2-8c6b-2bdb89159fee" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "", @@ -1880,7 +1820,7 @@ "output_name": "outfile" }, "input": { - "id": 2, + "id": 1, "output_name": "output" } }, @@ -1890,7 +1830,7 @@ "name": "how" } ], - "label": "Relabelled strand 2", + "label": "Relabelled strand 1", "name": "Relabel identifiers", "outputs": [ { @@ -1899,8 +1839,8 @@ } ], "position": { - "left": 1077, - "top": 324.99999999999994 + "left": 849.9999005376209, + "top": 365 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1913,15 +1853,9 @@ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "147ccbb0-b951-4851-9bf5-2c6b439ac1b6", + "uuid": "e9dcd2df-2834-4e9a-bef2-7666de012b8a", "when": null, - "workflow_outputs": [ - { - "label": "Relabelled strand 2", - "output_name": "output", - "uuid": "8ea49a28-635e-40c0-97d1-a8360f8347bf" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "", @@ -1930,11 +1864,11 @@ "id": 10, "input_connections": { "inputs_0|input": { - "id": 8, + "id": 9, "output_name": "output" }, "inputs_1|input": { - "id": 9, + "id": 8, "output_name": "output" } }, @@ -1948,8 +1882,8 @@ } ], "position": { - "left": 1360.7832000000906, - "top": 265.99999999999994 + "left": 1129.9999903467356, + "top": 120 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1987,8 +1921,8 @@ } ], "position": { - "left": 1624.7832000000903, - "top": 317.99999999999994 + "left": 1410.000136908115, + "top": 171 }, "post_job_actions": { "RenameDatasetActionout_file1": { @@ -2015,7 +1949,7 @@ } }, "tags": [], - "uuid": "879fffe0-897e-44c2-af76-934f0a79534c" + "uuid": "46c5d4bd-51e0-47c9-a2cf-3eafb2e26610" }, "tool_id": null, "type": "subworkflow", @@ -2397,8 +2331,8 @@ "name": "RNA-seq-Paired-QC", "outputs": [], "position": { - "left": 2357.58190526066, - "top": 409.2147543831772 + "left": 2355.578180184638, + "top": 506.20312678496407 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3117,8 +3051,8 @@ } ], "position": { - "left": 2385.207822325581, - "top": 904.4145593557384 + "left": 2361.203125, + "top": 970.40625 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -3165,6 +3099,6 @@ "tags": [ "RNAseq" ], - "uuid": "3855595a-2271-4c5a-b4dc-820a10fd3fd4", - "version": 26 + "uuid": "763f062e-7f5f-430a-9e11-78694f878e62", + "version": 32 } From 319638abdffae4d9c740a5d2f2870b06b327b366 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 15 Oct 2024 17:10:06 +0200 Subject: [PATCH 15/47] update sub workflows --- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 55 ++++++++++--------- 1 file changed, 29 insertions(+), 26 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 1d5501254..388ab4c30 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -732,8 +732,8 @@ } ], "position": { - "left": 1298.4945680301735, - "top": 1023.9750980404694 + "left": 1299.665360422669, + "top": 1023.9687008635165 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1", @@ -1068,16 +1068,19 @@ "format-version": "0.1", "license": "MIT", "name": "Get Uniquely mapped unstranded coverage", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, "steps": { "0": { - "annotation": "", + "annotation": "Mapped BAM files generate from RNA STAR", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "", + "description": "Mapped BAM files generate from RNA STAR", "name": "STAR BAM" } ], @@ -1097,14 +1100,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "", + "annotation": "RNA STAR log files", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "", + "description": "RNA STAR log files", "name": "STAR log" } ], @@ -1346,7 +1349,7 @@ "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { - "newname": "both strands coverage" + "newname": "Both Strands Coverage" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" @@ -1360,15 +1363,15 @@ "when": null, "workflow_outputs": [ { - "label": "both strands coverage", + "label": "both_strands_coverage", "output_name": "out_file1", - "uuid": "81faf6f8-1ec1-45f1-9e04-d2fd12a1ddc0" + "uuid": "e1696efa-645d-4160-9747-958b5893725f" } ] } }, "tags": [], - "uuid": "fdfcabc8-5014-4574-85ab-0182cb11750f" + "uuid": "3877b40c-3ede-42bd-ba6a-a9aa48ae6e74" }, "tool_id": null, "type": "subworkflow", @@ -1376,9 +1379,9 @@ "when": null, "workflow_outputs": [ { - "label": "both strands coverage", - "output_name": "both strands coverage", - "uuid": "9f2bf997-14f8-4307-90b4-dc068b02dcd6" + "label": "both_strands_coverage", + "output_name": "both_strands_coverage", + "uuid": "e067350a-7912-44c1-be48-66b9c6ce7713" } ] }, @@ -2156,15 +2159,15 @@ "uuid": "c38c3093-61e6-49f9-b756-8e25c37c8c68", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "transcripts_expression_cufflinks", - "output_name": "transcripts_expression", - "uuid": "bb2b3707-a64b-4fd6-801e-9d2ff1e3dbda" - }, { "label": "genes_expression_cufflinks", "output_name": "genes_expression", "uuid": "807a3d5e-8f42-43c2-a627-a4500c721939" + }, + { + "label": "transcripts_expression_cufflinks", + "output_name": "transcripts_expression", + "uuid": "bb2b3707-a64b-4fd6-801e-9d2ff1e3dbda" } ] }, @@ -3083,15 +3086,15 @@ "uuid": "61638ee7-d466-4b4b-988e-40f898041033", "when": null, "workflow_outputs": [ - { - "label": "deseq2_out", - "output_name": "deseq_out", - "uuid": "f2d85a14-6e83-4cbf-a34c-39b276e08acd" - }, { "label": "deseq2_plots", "output_name": "plots", "uuid": "318d01c1-ee47-4ba9-8474-f2e0f7e91b42" + }, + { + "label": "deseq2_out", + "output_name": "deseq_out", + "uuid": "f2d85a14-6e83-4cbf-a34c-39b276e08acd" } ] } @@ -3099,6 +3102,6 @@ "tags": [ "RNAseq" ], - "uuid": "763f062e-7f5f-430a-9e11-78694f878e62", - "version": 32 -} + "uuid": "3b2b7619-7ed9-4bb5-99dc-ab7ab633b931", + "version": 38 +} \ No newline at end of file From e5350c0c188a32a836ac6b812769451bff6440c6 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 16 Oct 2024 01:00:47 +0200 Subject: [PATCH 16/47] update tests --- .../rnaseq-pe/rnaseq-pe-tests.yml | 113 +++-- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 432 ++++++++++-------- ...ple_table.tabular => Sample table.tabular} | 0 3 files changed, 329 insertions(+), 216 deletions(-) rename workflows/transcriptomics/rnaseq-pe/test-data/{Sample_table.tabular => Sample table.tabular} (100%) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 8b6a1d651..a787695be 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -2,11 +2,11 @@ job: GTF file of annotation: class: File - location: https://zenodo.org/record/4541751/files/Drosophila_melanogaster.BDGP6.87.gtf + location: https://zenodo.org/records/13888221/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz filetype: gtf Sample table: class: File - path: test-data/Sample_table.tabular + path: test-data/Sample table.tabular filetype: tabular Collection paired FASTQ files: class: Collection @@ -52,70 +52,117 @@ - class: File identifier: reverse location: https://zenodo.org/records/13888221/files/GSM461181_2.fastqsanger + Generate QC reports?: true + Reference genome: dm6 Use featureCounts for generating count tables: true strandedness: unstranded Compute Cufflinks FPKM?: false GTF with regions to exclude from FPKM normalization with Cufflinks: null Compute StringTie FPKM?: true DEseq2 batch factors: null - Generate QC reports?: true - Reference genome: dm6 outputs: - deseq2_out: + Differential Expression Analysis using DESeq2: asserts: has_text_matching: expression: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" expression: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" - multiqc_stats: + DESeq2 Plots: + has_size: + size: 1784821 + delta: 100000 + MultiQC stats: asserts: has_text_matching: expression: "GSM461177\t0.406.*\t53.516.*\t6.1029\t0.516.*\t0.468.*\t90.67\t0.427.*\t82.73\t0.0409.*\t5.758.*\t14.114.*\t51.0\t35.980.*\t37\t10.0\t1.519.*" expression: "GSM461178\t0.403.*\t57.242.*\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" expression: "GSM461180\t0.3917.*\t55.727.*\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" expression: "GSM461181\t0.501.*\t58.451.*\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" - mapped_reads: + Mapped Reads: element_tests: GSM461177: - asserts: - has_size: - value: 45784586 - delta: 4000000 + has_size: + value: 45784586 + delta: 4000000 GSM461178: - asserts: - has_size: - value: 47832349 - delta: 4000000 + has_size: + value: 47832349 + delta: 4000000 GSM461180: - asserts: - has_size: - value: 48013469 - delta: 4000000 + has_size: + value: 48013469 + delta: 4000000 GSM461181: + has_size: + value: 53466524 + delta: 4000000 + Gene Abundance Estimates from StringTie: + element_tests: + GSM461177: asserts: - has_size: - value: 53466524 - delta: 4000000 - counts_table: + has_text: + text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" + FeatureCounts Summary Table: element_tests: + GSM461177: + asserts: + has_text: + text: "Assigned 406683" + GSM461178: + asserts: + has_text: + text: "Assigned 403016" GSM461180: asserts: has_text: - text: "FBgn0027948\t276" + text: "Assigned 391700" GSM461181: asserts: has_text: - text: "FBgn0027948\t297" - both strands coverage: + text: "Assigned 501807" + Coverage of Unstranded library: element_tests: GSM461177: - asserts: - has_size: - value: 5919847 - delta: 500000 - genes_expression_stringtie: + has_size: + value: 5919847 + delta: 300000 + GSM461178: + has_size: + value: 5573415 + delta: 250000 + GSM461180: + has_size: + value: 5650527 + delta: 250000 + GSM461181: + has_size: + value: 6688833 + delta: 300000 + Uniquely Mapped Stranded Coverage: element_tests: - GSM461177: + GSM461177_forward: + has_size: + value: 3097346 + delta: 150000 + GSM461181_forward: + has_size: + value: 3093571 + delta: 150000 + GSM461177_reverse: + has_size: + value: 3999045 + delta: 150000 + GSM461181_reverse: + has_size: + value: 3994419 + delta: 150000 + Counts Table: + element_tests: + GSM461180: asserts: has_text: - text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" + text: "FBgn0027948\t276" + GSM461181: + asserts: + has_text: + text: "FBgn0027948\t297" diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 388ab4c30..83d25cb0f 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -2,28 +2,6 @@ "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", "comments": [ - { - "child_steps": [ - 14, - 15, - 16, - 17 - ], - "color": "lime", - "data": { - "title": "Map Strandedness parameter" - }, - "id": 1, - "position": [ - 620.6, - 1208.9059588256873 - ], - "size": [ - 252.5, - 728.6 - ], - "type": "frame" - }, { "child_steps": [ 22, @@ -42,13 +20,35 @@ "id": 0, "position": [ 1001.6, - 838.5059588256875 + 841.5458406962506 ], "size": [ 1268, 696 ], "type": "frame" + }, + { + "child_steps": [ + 14, + 15, + 16, + 17 + ], + "color": "lime", + "data": { + "title": "Map Strandedness parameter" + }, + "id": 1, + "position": [ + 620.6, + 1211.9458406962506 + ], + "size": [ + 252.5, + 728.6 + ], + "type": "frame" } ], "creator": [ @@ -88,7 +88,7 @@ "outputs": [], "position": { "left": 0, - "top": 830.1582083386254 + "top": 833.1980902091885 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -115,7 +115,7 @@ "outputs": [], "position": { "left": 40, - "top": 940.1582083386254 + "top": 943.1980902091885 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -123,7 +123,13 @@ "type": "parameter_input", "uuid": "f3dcb910-684b-463d-bf98-03bc18451666", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "1591b48a-72b1-48d4-99d5-1cdcbc39a835" + } + ] }, "2": { "annotation": "Select the reference genome", @@ -142,7 +148,7 @@ "outputs": [], "position": { "left": 69.99997051198416, - "top": 1051.7939115602285 + "top": 1054.8337934307917 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -150,7 +156,13 @@ "type": "parameter_input", "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "eb735df9-5107-4950-af21-5cb1e1f43562" + } + ] }, "3": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", @@ -169,7 +181,7 @@ "outputs": [], "position": { "left": 119.99999475982484, - "top": 1148.9657432902018 + "top": 1152.005625160765 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -196,7 +208,7 @@ "outputs": [], "position": { "left": 159.66015029117847, - "top": 1257.6991448141564 + "top": 1260.7390266847196 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -204,7 +216,13 @@ "type": "parameter_input", "uuid": "8775ddf1-48f2-423e-813a-b5d302888580", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "8e126794-b297-41e3-965d-da2d9fe23929" + } + ] }, "5": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -223,7 +241,7 @@ "outputs": [], "position": { "left": 203.2055169930919, - "top": 1393.3511175991457 + "top": 1396.390999469709 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -231,7 +249,13 @@ "type": "parameter_input", "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "159c3f95-fced-4858-a595-316bb584067d" + } + ] }, "6": { "annotation": "This file will be used in MultiQC if the user opts out of featureCounts to generate count files. ", @@ -250,7 +274,7 @@ ], "position": { "left": 1021.6168910011272, - "top": 981.0332028479149 + "top": 984.0730847184781 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", @@ -284,7 +308,7 @@ "outputs": [], "position": { "left": 228.09439688484417, - "top": 1488.490577464827 + "top": 1491.5304593353903 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -292,7 +316,13 @@ "type": "parameter_input", "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "586880f1-62c3-4bce-b3d6-9850a714db3d" + } + ] }, "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -311,7 +341,7 @@ "outputs": [], "position": { "left": 259.4363655681731, - "top": 1606.778737326356 + "top": 1609.8186191969191 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -319,7 +349,13 @@ "type": "data_input", "uuid": "1d1b3d41-0efa-4ffa-aba9-0e80a51173a5", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "557447bf-c2cf-4030-8c6e-db5a90f8409b" + } + ] }, "9": { "annotation": "Whether FPKM values should be computed with StringTie", @@ -338,7 +374,7 @@ "outputs": [], "position": { "left": 268.103514973962, - "top": 1727.9661626467607 + "top": 1731.006044517324 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -346,7 +382,13 @@ "type": "parameter_input", "uuid": "47972cba-6df9-4883-8280-24ea28bcc4bb", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "437b5642-00ee-4516-b8e3-23e180417695" + } + ] }, "10": { "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. 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"name": "Stranded Coverage" + "name": "Coverage of Stranded libray" } ], - "label": "Stranded Coverage", + "label": "Coverage of Stranded libray", "name": "Re-arrange Stranded RNA-seq coverage", "outputs": [], "position": { - "left": 2355.558892204338, - "top": 188.4809790162957 + "left": 2363.2500148471677, + "top": 214.66773616189366 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1461,7 +1509,13 @@ "type": "parameter_input", "uuid": "56955f25-7e9e-4201-a056-b61f47359c84", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d363c181-7f37-45ef-9732-86aaf879478a" + } + ] }, "1": { "annotation": "From STAR strand 1", @@ -1944,15 +1998,15 @@ "when": null, "workflow_outputs": [ { - "label": "stranded coverage", + "label": "Uniquely Mapped Stranded Coverage", "output_name": "out_file1", - "uuid": "56ad2ce4-a0d8-4895-b774-79705460c246" + "uuid": "0a31ff80-b3d1-4959-869f-1a6a3c627dde" } ] } }, "tags": [], - "uuid": "46c5d4bd-51e0-47c9-a2cf-3eafb2e26610" + "uuid": "f5bde9df-1387-4d76-a90c-1043c93e8de5" }, "tool_id": null, "type": "subworkflow", @@ -1960,9 +2014,14 @@ "when": null, "workflow_outputs": [ { - 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"newname": "Transcripts expression from Cufflinks" + "newname": "Transcripts Expression from Cufflinks" }, "action_type": "RenameDatasetAction", "output_name": "transcripts_expression" @@ -2160,14 +2226,14 @@ "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "genes_expression_cufflinks", + "label": "Genes Expression from Cufflinks", "output_name": "genes_expression", - "uuid": "807a3d5e-8f42-43c2-a627-a4500c721939" + "uuid": "7716fdfa-3887-4c5a-8a60-6d8b13c1fbd4" }, { - "label": "transcripts_expression_cufflinks", + "label": "Transcripts Expression from Cufflinks", "output_name": "transcripts_expression", - "uuid": "bb2b3707-a64b-4fd6-801e-9d2ff1e3dbda" + "uuid": "be8f1022-5c63-4646-9c24-9368141eaa38" } ] }, @@ -2197,7 +2263,7 @@ ], "position": { "left": 2049.6016957581687, - "top": 925.813069095452 + "top": 928.8529509660151 }, "post_job_actions": { "RenameDatasetActiondata_param": { @@ -2222,9 +2288,9 @@ "when": null, "workflow_outputs": [ { - "label": "featurecounts_summary_table", + "label": "FeatureCounts Summary Table", "output_name": "data_param", - "uuid": "69c0c5b8-06ac-4f0f-b7d5-7947be783690" + "uuid": "8c15f8aa-f2eb-41bf-bbaa-947263f3bfec" } ] }, @@ -2254,7 +2320,7 @@ ], "position": { "left": 1766.5223844668794, - "top": 1186.4532253529665 + "top": 1189.4931072235297 }, "post_job_actions": { "RenameDatasetActiondata_param": { @@ -2279,9 +2345,9 @@ "when": null, "workflow_outputs": [ { - "label": "counts_table", + "label": "Counts Table", "output_name": "data_param", - "uuid": "57bef9ba-624b-4708-b40b-19fb8e8ee0b7" + "uuid": "9c6f7d5b-5462-4a09-b2e7-4f0577c99e5d" } ] }, @@ -2335,7 +2401,7 @@ "outputs": [], "position": { "left": 2355.578180184638, - "top": 506.20312678496407 + "top": 509.24300865552726 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2940,27 +3006,27 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"RuntimeValue\"}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 7, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"RuntimeValue\"}}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastqc\", \"__current_case__\": 8, \"output\": [{\"__index__\": 0, \"type\": \"data\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"cutadapt\", \"__current_case__\": 5, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 3, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"read_distribution\", \"__current_case__\": 6, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 4, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}, {\"__index__\": 5, \"software_cond\": {\"software\": \"rseqc\", \"__current_case__\": 22, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"gene_body_coverage\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 6, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"idxstats\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 7, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"Combined Quality Report \", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "b5e9c0d2-62f4-41b2-a1c7-5677d8555fd4", "when": null, "workflow_outputs": [ { - "label": "multiqc_stats", + "label": "MultiQC stats", "output_name": "stats", - "uuid": "cb34b85e-c36d-4dd3-8b29-640faa8357c6" + "uuid": "cbf99516-9349-4f2a-ad1f-05c732cb5263" }, { - "label": "multiqc_html_report", + "label": "MultiQC HTML report", "output_name": "html_report", - "uuid": "ba992ca2-42f2-4827-8a8c-0c8a756aeeb7" + "uuid": "7306cd4b-1017-4542-bf57-81d2d83d6a97" } ] } }, "tags": [], - "uuid": "d5726195-81e8-4d86-bc77-753f071e5dda" + "uuid": "7e9b1a51-ae8c-4cd6-b0fc-d31c5ef519ac" }, "tool_id": null, "type": "subworkflow", @@ -2968,14 +3034,14 @@ "when": "$(inputs.when)", "workflow_outputs": [ { - "label": "multiqc_html_report", - "output_name": "multiqc_html_report", - "uuid": "6cb02d1e-f8fa-480a-b019-edc686755d6e" + "label": "MultiQC stats", + "output_name": "MultiQC stats", + "uuid": "5edfd8e0-813b-4bbe-8cbd-a6042be2ab69" }, { - "label": "multiqc_stats", - "output_name": "multiqc_stats", - "uuid": "041c8433-ab5c-44bb-ac1b-eca2bf48fa94" + "label": "MultiQC HTML report", + "output_name": "MultiQC HTML report", + "uuid": "d6c186de-d392-43a4-8c05-54fc1f7968e0" } ] }, @@ -3005,7 +3071,7 @@ ], "position": { "left": 2041.3664627675912, - "top": 1244.3438104243314 + "top": 1247.3836922948947 }, "post_job_actions": {}, "tool_id": "__TAG_FROM_FILE__", @@ -3054,8 +3120,8 @@ } ], "position": { - "left": 2361.203125, - "top": 970.40625 + "left": 2357.0680264908797, + "top": 970.3448290748597 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -3067,7 +3133,7 @@ }, "RenameDatasetActionplots": { "action_arguments": { - "newname": "DESeq2 plots" + "newname": "DESeq2 Plots" }, "action_type": "RenameDatasetAction", "output_name": "plots" @@ -3087,14 +3153,14 @@ "when": null, "workflow_outputs": [ { - "label": "deseq2_plots", - "output_name": "plots", - "uuid": "318d01c1-ee47-4ba9-8474-f2e0f7e91b42" + "label": "Differential Expression Analysis using DESeq2", + "output_name": "deseq_out", + "uuid": "57699c23-58c6-4ff1-8fb2-98c2a2e82f00" }, { - "label": "deseq2_out", - "output_name": "deseq_out", - "uuid": "f2d85a14-6e83-4cbf-a34c-39b276e08acd" + "label": "DESeq2 Plots", + "output_name": "plots", + "uuid": "fba8ce87-d322-44b3-a217-53f6a1455225" } ] } @@ -3102,6 +3168,6 @@ "tags": [ "RNAseq" ], - "uuid": "3b2b7619-7ed9-4bb5-99dc-ab7ab633b931", - "version": 38 + "uuid": "7763d0dc-65d8-49da-8800-d12383385535", + "version": 51 } \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/test-data/Sample_table.tabular b/workflows/transcriptomics/rnaseq-pe/test-data/Sample table.tabular similarity index 100% rename from workflows/transcriptomics/rnaseq-pe/test-data/Sample_table.tabular rename to workflows/transcriptomics/rnaseq-pe/test-data/Sample table.tabular From aa48eae09624c3983210f12492f4416abcbed0e2 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 16 Oct 2024 01:41:40 +0200 Subject: [PATCH 17/47] replace gtf.gz with gtf --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index a787695be..2e84e9655 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -2,7 +2,7 @@ job: GTF file of annotation: class: File - location: https://zenodo.org/records/13888221/files/Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz + location: https://zenodo.org/record/4541751/files/Drosophila_melanogaster.BDGP6.87.gtf filetype: gtf Sample table: class: File From 9a3e23f19510938d65d77469438cd314732a1bae Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 16 Oct 2024 02:30:36 +0200 Subject: [PATCH 18/47] remove the subworkflow of rearraging coverage files --- .../rnaseq-pe/rnaseq-pe-tests.yml | 18 - .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1006 ++++------------- 2 files changed, 207 insertions(+), 817 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 2e84e9655..8f251356a 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -137,24 +137,6 @@ has_size: value: 6688833 delta: 300000 - Uniquely Mapped Stranded Coverage: - element_tests: - GSM461177_forward: - has_size: - value: 3097346 - delta: 150000 - GSM461181_forward: - has_size: - value: 3093571 - delta: 150000 - GSM461177_reverse: - has_size: - value: 3999045 - delta: 150000 - GSM461181_reverse: - has_size: - value: 3994419 - delta: 150000 Counts Table: element_tests: GSM461180: diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 83d25cb0f..7c79c80e2 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -2,15 +2,37 @@ "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", "comments": [ + { + "child_steps": [ + 14, + 15, + 16, + 17 + ], + "color": "lime", + "data": { + "title": "Map Strandedness parameter" + }, + "id": 1, + "position": [ + 620.6, + 1211.9458406962506 + ], + "size": [ + 252.5, + 728.6 + ], + "type": "frame" + }, { "child_steps": [ 22, + 26, 27, - 28, 21, 18, 6, - 30, + 29, 19 ], "color": "turquoise", @@ -27,28 +49,6 @@ 696 ], "type": "frame" - }, - { - "child_steps": [ - 14, - 15, - 16, - 17 - ], - "color": "lime", - "data": { - "title": "Map Strandedness parameter" - }, - "id": 1, - "position": [ - 620.6, - 1211.9458406962506 - ], - "size": [ - 252.5, - 728.6 - ], - "type": "frame" } ], "creator": [ @@ -1435,771 +1435,179 @@ }, "24": { "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", + "errors": null, "id": 24, "input_connections": { - "Bedgraph strand 1": { + "guide|guide_source|ref_hist": { + "id": 3, + "output_name": "output" + }, + "input_options|input_bam": { "id": 20, - "input_subworkflow_step_id": 1, - "output_name": "signal_unique_str1" + "output_name": "mapped_reads" + }, + "rna_strandness": { + "id": 16, + "output_name": "output_param_text" + }, + "when": { + "id": 9, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool StringTie", + "name": "adv" + }, + { + "description": "runtime parameter for tool StringTie", + "name": "input_options" + } + ], + "label": "Compute FPKM with StringTie", + "name": "StringTie", + "outputs": [ + { + "name": "output_gtf", + "type": "gtf" + }, + { + "name": "gene_abundance_estimation", + "type": "tabular" + } + ], + "position": { + "left": 2386.0764558032492, + "top": 1564.3828309664939 + }, + "post_job_actions": { + "HideDatasetActionoutput_gtf": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_gtf" + }, + "RenameDatasetActiongene_abundance_estimation": { + 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false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.3+galaxy0", - "type": "tool", - "uuid": "0403b248-c73c-4a1b-85fd-64f36278c952", - "when": "$(inputs.when)", - "workflow_outputs": [ - { - "label": "Gene Abundance Estimates from StringTie", - "output_name": "gene_abundance_estimation", - "uuid": "8a8f3ecc-9273-46ef-afd9-d74ebc423cb3" - } - ] - }, - "26": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", - "errors": null, - "id": 26, - "input_connections": { - "advanced_settings|library_type": { - "id": 15, - "output_name": "output_param_text" - }, - "advanced_settings|mask_file": { - "id": 8, - "output_name": "output" - }, - "bias_correction|seq_source|index": { - "id": 13, - "output_name": "out1" - }, - "input": { - "id": 20, - "output_name": "mapped_reads" - }, - "reference_annotation|reference_annotation_file": { - "id": 3, - "output_name": "output" - }, - "when": { - "id": 7, - "output_name": "output" - } - }, - "inputs": [ - { - "description": "runtime parameter for tool Cufflinks", - "name": "advanced_settings" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "advanced_settings" - }, - { - "description": "runtime parameter for tool Cufflinks", - "name": "reference_annotation" - } - ], - "label": "Compute FPKM with cufflinks", - "name": "Cufflinks", - "outputs": [ - { - "name": "genes_expression", - "type": "tabular" - }, - { - "name": "transcripts_expression", - "type": "tabular" - }, - { - "name": "assembled_isoforms", - "type": "gtf" - }, - { - "name": "total_map_mass", - "type": "txt" - }, - { - "name": "skipped", - "type": "gtf" - } - ], - "position": { - "left": 2396.799924469628, - "top": 1946.9544593506812 - }, - "post_job_actions": { - "HideDatasetActionassembled_isoforms": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "assembled_isoforms" - }, - "HideDatasetActionskipped": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "skipped" - }, - "HideDatasetActiontotal_map_mass": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "total_map_mass" - }, - "RenameDatasetActiongenes_expression": { - "action_arguments": { - "newname": "Genes Expression from Cufflinks" + "HideDatasetActionskipped": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "skipped" + }, + "HideDatasetActiontotal_map_mass": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "total_map_mass" + }, + "RenameDatasetActiongenes_expression": { + "action_arguments": { + "newname": "Genes Expression from Cufflinks" }, "action_type": "RenameDatasetAction", "output_name": "genes_expression" @@ -2225,23 +1633,23 @@ "uuid": "c38c3093-61e6-49f9-b756-8e25c37c8c68", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "Genes Expression from Cufflinks", - "output_name": "genes_expression", - "uuid": "7716fdfa-3887-4c5a-8a60-6d8b13c1fbd4" - }, { "label": "Transcripts Expression from Cufflinks", "output_name": "transcripts_expression", "uuid": "be8f1022-5c63-4646-9c24-9368141eaa38" + }, + { + "label": "Genes Expression from Cufflinks", + "output_name": "genes_expression", + "uuid": "7716fdfa-3887-4c5a-8a60-6d8b13c1fbd4" } ] }, - "27": { + "26": { "annotation": "featureCounts summaries", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 27, + "id": 26, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 21, @@ -2294,11 +1702,11 @@ } ] }, - "28": { + "27": { "annotation": "Counts Table ", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 28, + "id": 27, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 21, @@ -2351,9 +1759,9 @@ } ] }, - "29": { + "28": { "annotation": "", - "id": 29, + "id": 28, "input_connections": { "Cutadapt Reports": { "id": 12, @@ -2376,7 +1784,7 @@ "output_name": "mapped_reads" }, "featureCounts summaries": { - "id": 27, + "id": 26, "input_subworkflow_step_id": 1, "output_name": "data_param" }, @@ -3045,14 +2453,14 @@ } ] }, - "30": { + "29": { "annotation": "", "content_id": "__TAG_FROM_FILE__", "errors": null, - "id": 30, + "id": 29, "input_connections": { "input": { - "id": 28, + "id": 27, "output_name": "data_param" }, "tags": { @@ -3082,11 +2490,11 @@ "when": null, "workflow_outputs": [] }, - "31": { + "30": { "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0", "errors": null, - "id": 31, + "id": 30, "input_connections": { "batch_factors": { "id": 11, @@ -3097,7 +2505,7 @@ "output_name": "output" }, "select_data|countsFile": { - "id": 30, + "id": 29, "output_name": "output" } }, @@ -3152,15 +2560,15 @@ "uuid": "61638ee7-d466-4b4b-988e-40f898041033", "when": null, "workflow_outputs": [ - { - "label": "Differential Expression Analysis using DESeq2", - "output_name": "deseq_out", - "uuid": "57699c23-58c6-4ff1-8fb2-98c2a2e82f00" - }, { "label": "DESeq2 Plots", "output_name": "plots", "uuid": "fba8ce87-d322-44b3-a217-53f6a1455225" + }, + { + "label": "Differential Expression Analysis using DESeq2", + "output_name": "deseq_out", + "uuid": "57699c23-58c6-4ff1-8fb2-98c2a2e82f00" } ] } @@ -3168,6 +2576,6 @@ "tags": [ "RNAseq" ], - "uuid": "7763d0dc-65d8-49da-8800-d12383385535", - "version": 51 -} \ No newline at end of file + "uuid": "04f244ca-404b-4c56-96b6-187fe19e44b6", + "version": 52 +} From 9f8ead8d53715ba293e45e204f5dd109cb02d64e Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 16 Oct 2024 12:37:07 +0200 Subject: [PATCH 19/47] one more try --- .../rnaseq-pe/rnaseq-pe-tests.yml | 23 +++++++++---------- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 22 +++++++++--------- 2 files changed, 22 insertions(+), 23 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 8f251356a..71ad6a24c 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -95,6 +95,16 @@ has_size: value: 53466524 delta: 4000000 + Counts Table: + element_tests: + GSM461180: + asserts: + has_text: + text: "FBgn0027948\t276" + GSM461181: + asserts: + has_text: + text: "FBgn0027948\t297" Gene Abundance Estimates from StringTie: element_tests: GSM461177: @@ -136,15 +146,4 @@ GSM461181: has_size: value: 6688833 - delta: 300000 - Counts Table: - element_tests: - GSM461180: - asserts: - has_text: - text: "FBgn0027948\t276" - GSM461181: - asserts: - has_text: - text: "FBgn0027948\t297" - + delta: 300000 \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 7c79c80e2..f841fe368 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -127,7 +127,7 @@ { "label": null, "output_name": "output", - "uuid": "1591b48a-72b1-48d4-99d5-1cdcbc39a835" + "uuid": "70e2c0a9-8f14-4cfb-a519-da3d38d4703e" } ] }, @@ -160,7 +160,7 @@ { "label": null, "output_name": "output", - "uuid": "eb735df9-5107-4950-af21-5cb1e1f43562" + "uuid": "c9707423-628e-41e9-93ce-bb1790d02fb2" } ] }, @@ -220,7 +220,7 @@ { "label": null, "output_name": "output", - "uuid": "8e126794-b297-41e3-965d-da2d9fe23929" + "uuid": "cef66658-2ba6-4996-8bf4-11d245db8a85" } ] }, @@ -253,7 +253,7 @@ { "label": null, "output_name": "output", - "uuid": "159c3f95-fced-4858-a595-316bb584067d" + "uuid": "5c971093-414e-4b1c-b315-96cbcc7f5da1" } ] }, @@ -320,7 +320,7 @@ { "label": null, "output_name": "output", - "uuid": "586880f1-62c3-4bce-b3d6-9850a714db3d" + "uuid": "b00147ff-b44e-4679-a05b-18321b2f270e" } ] }, @@ -353,7 +353,7 @@ { "label": null, "output_name": "output", - "uuid": "557447bf-c2cf-4030-8c6e-db5a90f8409b" + "uuid": "58be0511-0a5c-4370-8cc4-39e27378e9d5" } ] }, @@ -386,7 +386,7 @@ { "label": null, "output_name": "output", - "uuid": "437b5642-00ee-4516-b8e3-23e180417695" + "uuid": "6d55ee86-8552-408c-88eb-6e75487d5e9c" } ] }, @@ -446,7 +446,7 @@ { "label": null, "output_name": "output", - "uuid": "ed41ecc4-41bf-421e-9eb9-3396427e3181" + "uuid": "ad3f9e9e-15d5-4ccd-8879-89ff178c5215" } ] }, @@ -2576,6 +2576,6 @@ "tags": [ "RNAseq" ], - "uuid": "04f244ca-404b-4c56-96b6-187fe19e44b6", - "version": 52 -} + "uuid": "1839940b-5ddd-41ab-9897-9d46f3390006", + "version": 53 +} \ No newline at end of file From 08dd45b87bca5744a331885646a9f32b872d076f Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 16 Oct 2024 15:40:54 +0200 Subject: [PATCH 20/47] update test asserts --- .../rnaseq-pe/rnaseq-pe-tests.yml | 54 +++++++++++-------- 1 file changed, 33 insertions(+), 21 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 71ad6a24c..6b4adab0d 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -64,36 +64,36 @@ Differential Expression Analysis using DESeq2: asserts: has_text_matching: - expression: "FBgn0003360\t103.508.*\t-3.005*\t0.333.*\t-9.022.*\t1.832.*\t2.041.*" - expression: "FBgn0266599\t3014.611.*\t0.288.*\t0.122.*\t2.354.*\t0.018.*\t0.393.*" + expression: "FBgn0003360\t112.56[0-9]*\t-3.14[0-9]*\t0.32[0-9]*\t-9.76[0-9]*\t1.60[0-9]*e-[0-9]*\t1.51[0-9]*e-[0-9]*" + expression: "FBgn0266599\t3016.67[0-9]*\t0.28[0-9]*\t0.12[0-9]*\t2.32[0-9]*\t0.019[0-9]*\t0.35[0-9]*" DESeq2 Plots: has_size: - size: 1784821 + size: 1734460 delta: 100000 MultiQC stats: asserts: has_text_matching: - expression: "GSM461177\t0.406.*\t53.516.*\t6.1029\t0.516.*\t0.468.*\t90.67\t0.427.*\t82.73\t0.0409.*\t5.758.*\t14.114.*\t51.0\t35.980.*\t37\t10.0\t1.519.*" - expression: "GSM461178\t0.403.*\t57.242.*\t8.4144\t0.505.*\t0.454.*\t90.0\t0.420.*\t83.26\t0.034.*\t26.941.*\t11.777.*\t52.0\t33.188.*\t36\t10.0\t1.401.*" - expression: "GSM461180\t0.3917.*\t55.727.*\t6.5537\t0.509.*\t0.444.*\t87.31\t0.409.*\t80.37\t0.035.*\t24.543.*\t13.200.*\t52.0\t33.921.*\t37\t10.0\t1.399.*" - expression: "GSM461181\t0.501.*\t58.451.*\t7.878.*\t0.614.*\t0.563.*\t91.789.*\t0.523.*\t85.24\t0.0402.*\t6.077.*\t16.190.*\t53.0\t35.524.*\t37\t0.0\t1.715.*" + expression: "GSM461177\t0.40[0-9]*\t53.41[0-9]*\t6.10[0-9]*\t0.51[0-9]*\t0.46[0-9]*\t90.66[0-9]*\t0.42[0-9]*\t82.72\t0.041[0-9]*\t5.75[0-9]*\t14.11[0-9]*\t51.0\t35.98[0-9]*\t37\t10.0\t1.51[0-9]*" + expression: "GSM461178\t0.40[0-9]*\t57.13[0-9]*\t8.41[0-9]*\t0.50[0-9]*\t0.45[0-9]*\t90.0[0-9]*\t0.42[0-9]*\t83.26\t0.03[0-9]*\t26.94[0-9]*\t11.77[0-9]*\t52.0\t33.18[0-9]*\t36\t10.0\t1.40[0-9]*" + expression: "GSM461180\t0.39[0-9]*\t55.57[0-9]*\t6.55[0-9]*\t0.50[0-9]*\t0.44[0-9]*\t87.32[0-9]*\t0.40[0-9]*\t80.37\t0.03[0-9]*\t24.54[0-9]*\t13.19[0-9]*\t52.0\t33.92[0-9]*\t37\t10.0\t1.40[0-9]*" + expression: "GSM461181\t0.50[0-9]*\t58.37[0-9]*\t7.87[0-9]*\t0.61[0-9]*\t0.56[0-9]*\t91.78[0-9]*\t0.52[0-9]*\t85.24\t0.040[0-9]*\t6.07[0-9]*\t16.18[0-9]*\t53.0\t35.52[0-9]*\t37\t0.0\t1.71[0-9]*" Mapped Reads: element_tests: GSM461177: has_size: - value: 45784586 + value: 45786533 delta: 4000000 GSM461178: has_size: - value: 47832349 + value: 47835106 delta: 4000000 GSM461180: has_size: - value: 48013469 + value: 48022461 delta: 4000000 GSM461181: has_size: - value: 53466524 + value: 53477748 delta: 4000000 Counts Table: element_tests: @@ -109,41 +109,53 @@ element_tests: GSM461177: asserts: - has_text: - text: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.406286\t47.329643\t100.406349" + has_text_matching: + expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.40[0-9]*\t49.72[0-9]*\t102.64[0-9]*" + GSM461178: + asserts: + has_text_matching: + expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.16[0-9]*\t45.47[0-9]*\t84.16[0-9]*" + GSM461180: + asserts: + has_text_matching: + expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t0.00[0-9]*\t0.00[0-9]*\t0.00[0-9]*" + GSM461181: + asserts: + has_text_matching: + expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.48[0-9]*\t66.43[0-9]*\t122.54[0-9]*" FeatureCounts Summary Table: element_tests: GSM461177: asserts: has_text: - text: "Assigned 406683" + text: "Assigned\t405934" GSM461178: asserts: has_text: - text: "Assigned 403016" + text: "Assigned\t402322" GSM461180: asserts: has_text: - text: "Assigned 391700" + text: "Assigned\t390670" GSM461181: asserts: has_text: - text: "Assigned 501807" + text: "Assigned\t501297" Coverage of Unstranded library: element_tests: GSM461177: has_size: - value: 5919847 + value: 5921419 delta: 300000 GSM461178: has_size: - value: 5573415 + value: 5573303 delta: 250000 GSM461180: has_size: - value: 5650527 + value: 5655990 delta: 250000 GSM461181: has_size: - value: 6688833 + value: 6659698 delta: 300000 \ No newline at end of file From 3115d2177b15d9ffd6814e5d1e69403a4290957e Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 18 Oct 2024 14:44:50 +0200 Subject: [PATCH 21/47] add smaller test data and reduce the DESeq2 version to before betapriors option introduced --- .../rnaseq-pe/rnaseq-pe-tests.yml | 156 ++-- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 674 ++++++++++++++++-- 2 files changed, 732 insertions(+), 98 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 6b4adab0d..9fa3b7e97 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -6,7 +6,7 @@ filetype: gtf Sample table: class: File - path: test-data/Sample table.tabular + location: https://zenodo.org/records/13951092/files//Sample_table.tabular filetype: tabular Collection paired FASTQ files: class: Collection @@ -18,40 +18,40 @@ elements: - class: File identifier: forward - location: https://zenodo.org/records/13888221/files/GSM461177_1.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461177_1.fastqsanger - class: File identifier: reverse - location: https://zenodo.org/records/13888221/files/GSM461177_2.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461177_2.fastqsanger - class: Collection type: paired identifier: GSM461178 elements: - class: File identifier: forward - location: https://zenodo.org/records/13888221/files/GSM461178_1.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461178_1.fastqsanger - class: File identifier: reverse - location: https://zenodo.org/records/13888221/files/GSM461178_2.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461178_2.fastqsanger - class: Collection type: paired identifier: GSM461180 elements: - class: File identifier: forward - location: https://zenodo.org/records/13888221/files/GSM461180_1.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461180_1.fastqsanger - class: File identifier: reverse - location: https://zenodo.org/records/13888221/files/GSM461180_2.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461180_2.fastqsanger - class: Collection type: paired identifier: GSM461181 elements: - class: File identifier: forward - location: https://zenodo.org/records/13888221/files/GSM461181_1.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461181_1.fastqsanger - class: File identifier: reverse - location: https://zenodo.org/records/13888221/files/GSM461181_2.fastqsanger + location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger Generate QC reports?: true Reference genome: dm6 Use featureCounts for generating count tables: true @@ -61,101 +61,143 @@ Compute StringTie FPKM?: true DEseq2 batch factors: null outputs: + MultiQC stats: + asserts: + has_text_matching: + expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*\t39.93[0-9]*\t43.0\t36.44[0-9]*\t37\t10.0\t0.11[0-9]*" + expression: "GSM461178\t0.03[0-9]*\t81.76[0-9]*\t1.23[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t98.44\t0.04[0-9]*\t95.31\t0.00[0-9]*\t15.03[0-9]*\t29.82[0-9]*\t44.0\t34.37[0-9]*\t37\t10.0\t0.09[0-9]*" + expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*\t28.13[0-9]*\t44.0\t34.64[0-9]*\t37\t10.0\t0.09[0-9]*" + expression: "GSM461181\t0.04[0-9]*\t82.12[0-9]*\t0.71[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t99.13\t0.04[0-9]*\t96.24\t0.00[0-9]*\t2.90[0-9]*\t37.93[0-9]*\t44.0\t36.06[0-9]*\t37\t10.0\t0.10[0-9]*" Differential Expression Analysis using DESeq2: asserts: has_text_matching: - expression: "FBgn0003360\t112.56[0-9]*\t-3.14[0-9]*\t0.32[0-9]*\t-9.76[0-9]*\t1.60[0-9]*e-[0-9]*\t1.51[0-9]*e-[0-9]*" - expression: "FBgn0266599\t3016.67[0-9]*\t0.28[0-9]*\t0.12[0-9]*\t2.32[0-9]*\t0.019[0-9]*\t0.35[0-9]*" + expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" + expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" DESeq2 Plots: has_size: - size: 1734460 - delta: 100000 - MultiQC stats: - asserts: - has_text_matching: - expression: "GSM461177\t0.40[0-9]*\t53.41[0-9]*\t6.10[0-9]*\t0.51[0-9]*\t0.46[0-9]*\t90.66[0-9]*\t0.42[0-9]*\t82.72\t0.041[0-9]*\t5.75[0-9]*\t14.11[0-9]*\t51.0\t35.98[0-9]*\t37\t10.0\t1.51[0-9]*" - expression: "GSM461178\t0.40[0-9]*\t57.13[0-9]*\t8.41[0-9]*\t0.50[0-9]*\t0.45[0-9]*\t90.0[0-9]*\t0.42[0-9]*\t83.26\t0.03[0-9]*\t26.94[0-9]*\t11.77[0-9]*\t52.0\t33.18[0-9]*\t36\t10.0\t1.40[0-9]*" - expression: "GSM461180\t0.39[0-9]*\t55.57[0-9]*\t6.55[0-9]*\t0.50[0-9]*\t0.44[0-9]*\t87.32[0-9]*\t0.40[0-9]*\t80.37\t0.03[0-9]*\t24.54[0-9]*\t13.19[0-9]*\t52.0\t33.92[0-9]*\t37\t10.0\t1.40[0-9]*" - expression: "GSM461181\t0.50[0-9]*\t58.37[0-9]*\t7.87[0-9]*\t0.61[0-9]*\t0.56[0-9]*\t91.78[0-9]*\t0.52[0-9]*\t85.24\t0.040[0-9]*\t6.07[0-9]*\t16.18[0-9]*\t53.0\t35.52[0-9]*\t37\t0.0\t1.71[0-9]*" - Mapped Reads: + size: 33420 + delta: 1500 + Counts Table: + element_tests: + GSM461177: + asserts: + has_text: + text: "FBgn0017545\t6109" + GSM461178: + asserts: + has_text: + text: "FBgn0017545\t5649" + GSM461180: + asserts: + has_text: + text: "FBgn0017545\t5600" + GSM461181: + asserts: + has_text: + text: "FBgn0017545\t5943" + Coverage of Unstranded library: element_tests: GSM461177: has_size: - value: 45786533 - delta: 4000000 + value: 445281 + delta: 20000 GSM461178: has_size: - value: 47835106 - delta: 4000000 + value: 406443 + delta: 20000 GSM461180: has_size: - value: 48022461 - delta: 4000000 + value: 423518 + delta: 20000 GSM461181: has_size: - value: 53477748 - delta: 4000000 - Counts Table: + value: 455334 + delta: 20000 + Mapped Reads: element_tests: + GSM461177: + has_size: + value: 3058282 + delta: 150000 + GSM461178: + has_size: + value: 3032322 + delta: 150000 GSM461180: - asserts: - has_text: - text: "FBgn0027948\t276" + has_size: + value: 3165439 + delta: 150000 GSM461181: - asserts: - has_text: - text: "FBgn0027948\t297" + has_size: + value: 3075214 + delta: 150000 Gene Abundance Estimates from StringTie: element_tests: GSM461177: asserts: has_text_matching: - expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.40[0-9]*\t49.72[0-9]*\t102.64[0-9]*" + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" GSM461178: asserts: has_text_matching: - expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.16[0-9]*\t45.47[0-9]*\t84.16[0-9]*" + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t286.68[0-9]*\t143296.84[0-9]*\t365993.15[0-9]*" GSM461180: asserts: has_text_matching: - expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t0.00[0-9]*\t0.00[0-9]*\t0.00[0-9]*" + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t282.60[0-9]*\t138208.90[0-9]*\t367356.56[0-9]*" GSM461181: asserts: has_text_matching: - expression: "FBgn0031220\tCG4822\tchr2L\t-\t116970\t121754\t1.48[0-9]*\t66.43[0-9]*\t122.54[0-9]*" + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" FeatureCounts Summary Table: element_tests: GSM461177: asserts: has_text: - text: "Assigned\t405934" + text: "Assigned\t45715" GSM461178: asserts: has_text: - text: "Assigned\t402322" + text: "Assigned\t38738" GSM461180: asserts: has_text: - text: "Assigned\t390670" + text: "Assigned\t39998" GSM461181: asserts: has_text: - text: "Assigned\t501297" - Coverage of Unstranded library: + text: "Assigned\t44734" + Coverage of Stranded libray: element_tests: - GSM461177: + GSM461177_forward: has_size: - value: 5921419 - delta: 300000 - GSM461178: + value: 313382 + delta: 15000 + GSM461178_forward: has_size: - value: 5573303 - delta: 250000 - GSM461180: + value: 285608 + delta: 15000 + GSM461180_forward: has_size: - value: 5655990 - delta: 250000 - GSM461181: + value: 295650 + delta: 15000 + GSM461181_forward: + has_size: + value: 3075214 + delta: 15000 + GSM461177_reverse: + has_size: + value: 313241 + delta: 15000 + GSM461178_reverse: + has_size: + value: 281153 + delta: 15000 + GSM461180_reverse: + has_size: + value: 292239 + delta: 15000 + GSM461181_reverse: has_size: - value: 6659698 - delta: 300000 \ No newline at end of file + value: 322248 + delta: 15000 diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index f841fe368..fd67adc19 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -27,12 +27,12 @@ { "child_steps": [ 22, - 26, 27, + 28, 21, 18, 6, - 29, + 30, 19 ], "color": "turquoise", @@ -127,7 +127,7 @@ { "label": null, "output_name": "output", - "uuid": "70e2c0a9-8f14-4cfb-a519-da3d38d4703e" + "uuid": "84b6f01e-1961-44a8-8f8e-ae0d9c109b10" } ] }, @@ -160,7 +160,7 @@ { "label": null, "output_name": "output", - "uuid": "c9707423-628e-41e9-93ce-bb1790d02fb2" + "uuid": "b832bfb0-76e0-48da-b7f4-69914a3547c3" } ] }, @@ -220,7 +220,7 @@ { "label": null, "output_name": "output", - "uuid": "cef66658-2ba6-4996-8bf4-11d245db8a85" + "uuid": "2f8a38ff-9ff0-427e-ae9b-41f00589d09b" } ] }, @@ -253,7 +253,7 @@ { "label": null, "output_name": "output", - "uuid": "5c971093-414e-4b1c-b315-96cbcc7f5da1" + "uuid": "50b04716-1813-4de2-bb70-95c0a63773ca" } ] }, @@ -320,7 +320,7 @@ { "label": null, "output_name": "output", - "uuid": "b00147ff-b44e-4679-a05b-18321b2f270e" + "uuid": "342449e3-c0d2-497f-9dbe-652e73216daf" } ] }, @@ -353,7 +353,7 @@ { "label": null, "output_name": "output", - "uuid": "58be0511-0a5c-4370-8cc4-39e27378e9d5" + "uuid": "e318e33f-e914-41f4-a09c-e88a08d446c7" } ] }, @@ -386,7 +386,7 @@ { "label": null, "output_name": "output", - "uuid": "6d55ee86-8552-408c-88eb-6e75487d5e9c" + "uuid": "6e2cbf0c-707e-4cce-9254-52ff3214cc68" } ] }, @@ -446,7 +446,7 @@ { "label": null, "output_name": "output", - "uuid": "ad3f9e9e-15d5-4ccd-8879-89ff178c5215" + "uuid": "cf9e3e06-320c-47b7-b9e2-5222e0229c25" } ] }, @@ -1092,10 +1092,10 @@ "inputs": [ { "description": "", - "name": "Coverage of Unstranded library" + "name": "Generate Coverage of Unstranded library" } ], - "label": "Coverage of Unstranded library", + "label": "Generate Coverage of Unstranded library", "name": "Get Uniquely mapped unstranded coverage", "outputs": [], "position": { @@ -1429,15 +1429,607 @@ { "label": "Coverage of Unstranded library", "output_name": "Both Strands Coverage", - "uuid": "8b8e8f7f-04d8-4b5f-873b-0a62af98a3d4" + "uuid": "8376f1dd-6c9e-4328-a6f1-ebed29f235ff" } ] }, "24": { + "annotation": "", + "id": 24, + "input_connections": { + "Bedgraph strand 1": { + "id": 20, + "input_subworkflow_step_id": 1, + "output_name": "signal_unique_str1" + }, + "Bedgraph strand 2": { + "id": 20, + "input_subworkflow_step_id": 2, + "output_name": "signal_unique_str2" + }, + "strandedness": { + "id": 5, + "input_subworkflow_step_id": 0, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "", + "name": "Generate Coverage of Stranded libray" + } + ], + "label": "Generate Coverage of Stranded libray", + "name": "Re-arrange Stranded RNA-seq coverage", + "outputs": [], + "position": { + "left": 2354.25, + "top": 239.65625 + }, + "subworkflow": { + "a_galaxy_workflow": "true", + "annotation": "", + "comments": [], + "creator": [ + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-1964-4960", + "name": "Lucille Delisle" + } + ], + "format-version": "0.1", + "license": "MIT", + "name": "Re-arrange Stranded RNA-seq coverage", + "report": { + "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" + }, + "steps": { + "0": { + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "content_id": null, + "errors": null, + "id": 0, + "input_connections": {}, + "inputs": [ + { + "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "name": "strandedness" + } + ], + "label": "strandedness", + "name": "Input 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"input_connections": { "guide|guide_source|ref_hist": { "id": 3, @@ -1516,11 +2108,11 @@ } ] }, - "25": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", "errors": null, - "id": 25, + "id": 26, "input_connections": { "advanced_settings|library_type": { "id": 15, @@ -1645,11 +2237,11 @@ } ] }, - "26": { + "27": { "annotation": "featureCounts summaries", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 26, + "id": 27, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 21, @@ -1702,11 +2294,11 @@ } ] }, - "27": { + "28": { "annotation": "Counts Table ", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 27, + "id": 28, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 21, @@ -1759,9 +2351,9 @@ } ] }, - "28": { + "29": { "annotation": "", - "id": 28, + "id": 29, "input_connections": { "Cutadapt Reports": { "id": 12, @@ -1784,7 +2376,7 @@ "output_name": "mapped_reads" }, "featureCounts summaries": { - "id": 26, + "id": 27, "input_subworkflow_step_id": 1, "output_name": "data_param" }, @@ -2453,14 +3045,14 @@ } ] }, - "29": { + "30": { "annotation": "", "content_id": "__TAG_FROM_FILE__", "errors": null, - "id": 29, + "id": 30, "input_connections": { "input": { - "id": 27, + "id": 28, "output_name": "data_param" }, "tags": { @@ -2490,11 +3082,11 @@ "when": null, "workflow_outputs": [] }, - "30": { + "31": { "annotation": "Count files have a header if featureCounts is used.", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "errors": null, - "id": 30, + "id": 31, "input_connections": { "batch_factors": { "id": 11, @@ -2505,7 +3097,7 @@ "output_name": "output" }, "select_data|countsFile": { - "id": 29, + "id": 30, "output_name": "output" } }, @@ 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{\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.11.40.7+galaxy2", "type": "tool", "uuid": "61638ee7-d466-4b4b-988e-40f898041033", "when": null, "workflow_outputs": [ - { - "label": "DESeq2 Plots", - "output_name": "plots", - "uuid": "fba8ce87-d322-44b3-a217-53f6a1455225" - }, { "label": "Differential Expression Analysis using DESeq2", "output_name": "deseq_out", "uuid": "57699c23-58c6-4ff1-8fb2-98c2a2e82f00" + }, + { + "label": "DESeq2 Plots", + "output_name": "plots", + "uuid": "fba8ce87-d322-44b3-a217-53f6a1455225" } ] } @@ -2576,6 +3168,6 @@ "tags": [ "RNAseq" ], - "uuid": "1839940b-5ddd-41ab-9897-9d46f3390006", - "version": 53 + "uuid": "9a750a3f-7d7c-4fb3-9784-269d61511508", + "version": 55 } \ No newline at end of file From 082c57a8cfcb4407cc58db8fe851797b22c19e9b Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 18 Oct 2024 15:25:16 +0200 Subject: [PATCH 22/47] remove subworkflows --- .../rnaseq-pe/rnaseq-pe-tests.yml | 61 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1885 +---------------- 2 files changed, 96 insertions(+), 1850 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 9fa3b7e97..1c81a363e 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -61,13 +61,6 @@ Compute StringTie FPKM?: true DEseq2 batch factors: null outputs: - MultiQC stats: - asserts: - has_text_matching: - expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*\t39.93[0-9]*\t43.0\t36.44[0-9]*\t37\t10.0\t0.11[0-9]*" - expression: "GSM461178\t0.03[0-9]*\t81.76[0-9]*\t1.23[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t98.44\t0.04[0-9]*\t95.31\t0.00[0-9]*\t15.03[0-9]*\t29.82[0-9]*\t44.0\t34.37[0-9]*\t37\t10.0\t0.09[0-9]*" - expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*\t28.13[0-9]*\t44.0\t34.64[0-9]*\t37\t10.0\t0.09[0-9]*" - expression: "GSM461181\t0.04[0-9]*\t82.12[0-9]*\t0.71[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t99.13\t0.04[0-9]*\t96.24\t0.00[0-9]*\t2.90[0-9]*\t37.93[0-9]*\t44.0\t36.06[0-9]*\t37\t10.0\t0.10[0-9]*" Differential Expression Analysis using DESeq2: asserts: has_text_matching: @@ -95,24 +88,6 @@ asserts: has_text: text: "FBgn0017545\t5943" - Coverage of Unstranded library: - element_tests: - GSM461177: - has_size: - value: 445281 - delta: 20000 - GSM461178: - has_size: - value: 406443 - delta: 20000 - GSM461180: - has_size: - value: 423518 - delta: 20000 - GSM461181: - has_size: - value: 455334 - delta: 20000 Mapped Reads: element_tests: GSM461177: @@ -166,38 +141,4 @@ GSM461181: asserts: has_text: - text: "Assigned\t44734" - Coverage of Stranded libray: - element_tests: - GSM461177_forward: - has_size: - value: 313382 - delta: 15000 - GSM461178_forward: - has_size: - value: 285608 - delta: 15000 - GSM461180_forward: - has_size: - value: 295650 - delta: 15000 - GSM461181_forward: - has_size: - value: 3075214 - delta: 15000 - GSM461177_reverse: - has_size: - value: 313241 - delta: 15000 - GSM461178_reverse: - has_size: - value: 281153 - delta: 15000 - GSM461180_reverse: - has_size: - value: 292239 - delta: 15000 - GSM461181_reverse: - has_size: - value: 322248 - delta: 15000 + text: "Assigned\t44734" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index fd67adc19..fd832843a 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -13,10 +13,10 @@ "data": { "title": "Map Strandedness parameter" }, - "id": 1, + "id": 0, "position": [ 620.6, - 1211.9458406962506 + 799.4609386533648 ], "size": [ 252.5, @@ -27,22 +27,21 @@ { "child_steps": [ 22, - 27, - 28, + 25, + 26, 21, 18, - 6, - 30, + 7, 19 ], "color": "turquoise", "data": { "title": "Count table processing" }, - "id": 0, + "id": 1, "position": [ 1001.6, - 841.5458406962506 + 429.06093865336476 ], "size": [ 1268, @@ -65,7 +64,6 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.10", "name": "RNAseq_PE", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -88,7 +86,7 @@ "outputs": [], "position": { "left": 0, - "top": 833.1980902091885 + "top": 420.7131881663027 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -115,7 +113,7 @@ "outputs": [], "position": { "left": 40, - "top": 943.1980902091885 + "top": 530.7131881663026 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -123,13 +121,7 @@ "type": "parameter_input", "uuid": "f3dcb910-684b-463d-bf98-03bc18451666", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "84b6f01e-1961-44a8-8f8e-ae0d9c109b10" - } - ] + "workflow_outputs": [] }, "2": { "annotation": "Select the reference genome", @@ -148,7 +140,7 @@ "outputs": [], "position": { "left": 69.99997051198416, - "top": 1054.8337934307917 + "top": 642.348891387906 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -156,13 +148,7 @@ "type": "parameter_input", "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "b832bfb0-76e0-48da-b7f4-69914a3547c3" - } - ] + "workflow_outputs": [] }, "3": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", @@ -181,7 +167,7 @@ "outputs": [], "position": { "left": 119.99999475982484, - "top": 1152.005625160765 + "top": 739.5207231178792 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -208,7 +194,7 @@ "outputs": [], "position": { "left": 159.66015029117847, - "top": 1260.7390266847196 + "top": 848.2541246418339 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -216,13 +202,7 @@ "type": "parameter_input", "uuid": "8775ddf1-48f2-423e-813a-b5d302888580", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "2f8a38ff-9ff0-427e-ae9b-41f00589d09b" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", @@ -241,7 +221,7 @@ "outputs": [], "position": { "left": 203.2055169930919, - "top": 1396.390999469709 + "top": 983.9060974268232 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -249,19 +229,40 @@ "type": "parameter_input", "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", "when": null, - "workflow_outputs": [ + "workflow_outputs": [] + }, + "6": { + "annotation": "Whether FPKM values should be computed with Cufflinks", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ { - "label": null, - "output_name": "output", - "uuid": "50b04716-1813-4de2-bb70-95c0a63773ca" + "description": "Whether FPKM values should be computed with Cufflinks", + "name": "Compute Cufflinks FPKM?" } - ] + ], + "label": "Compute Cufflinks FPKM?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 228.09439688484417, + "top": 1079.0455572925046 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", + "when": null, + "workflow_outputs": [] }, - "6": { + "7": { "annotation": "This file will be used in MultiQC if the user opts out of featureCounts to generate count files. ", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", "errors": null, - "id": 6, + "id": 7, "input_connections": {}, "inputs": [], "label": "A dummy featureCounts summary file", @@ -273,8 +274,8 @@ } ], "position": { - "left": 1021.6168910011272, - "top": 984.0730847184781 + "left": 1004.8723555819801, + "top": 618.9988773615364 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", @@ -291,39 +292,6 @@ "when": null, "workflow_outputs": [] }, - "7": { - "annotation": "Whether FPKM values should be computed with Cufflinks", - "content_id": null, - "errors": null, - "id": 7, - "input_connections": {}, - "inputs": [ - { - "description": "Whether FPKM values should be computed with Cufflinks", - "name": "Compute Cufflinks FPKM?" - } - ], - "label": "Compute Cufflinks FPKM?", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 228.09439688484417, - "top": 1491.5304593353903 - }, - "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", - "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "342449e3-c0d2-497f-9dbe-652e73216daf" - } - ] - }, "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, @@ -341,7 +309,7 @@ "outputs": [], "position": { "left": 259.4363655681731, - "top": 1609.8186191969191 + "top": 1197.3337171540334 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -349,13 +317,7 @@ "type": "data_input", "uuid": "1d1b3d41-0efa-4ffa-aba9-0e80a51173a5", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "e318e33f-e914-41f4-a09c-e88a08d446c7" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "Whether FPKM values should be computed with StringTie", @@ -374,7 +336,7 @@ "outputs": [], "position": { "left": 268.103514973962, - "top": 1731.006044517324 + "top": 1318.5211424744382 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -382,13 +344,7 @@ "type": "parameter_input", "uuid": "47972cba-6df9-4883-8280-24ea28bcc4bb", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "6e2cbf0c-707e-4cce-9254-52ff3214cc68" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", @@ -407,7 +363,7 @@ "outputs": [], "position": { "left": 271.9528882100886, - "top": 1825.7688556891108 + "top": 1413.283953646225 }, "tool_id": null, "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", @@ -434,7 +390,7 @@ "outputs": [], "position": { "left": 1906.3299807760093, - "top": 1642.3453537153487 + "top": 1229.860451672463 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": null}", @@ -442,13 +398,7 @@ "type": "data_input", "uuid": "96d02185-64bb-4d77-b986-cc6209329334", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "cf9e3e06-320c-47b7-b9e2-5222e0229c25" - } - ] + "workflow_outputs": [] }, "12": { "annotation": "", @@ -481,7 +431,7 @@ ], "position": { "left": 310.957760903539, - "top": 656.2466428328726 + "top": 243.76174078998673 }, "post_job_actions": { "HideDatasetActionout1": { @@ -536,7 +486,7 @@ ], "position": { "left": 785.2116386388172, - 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"annotation": "", - "id": 23, - "input_connections": { - "STAR BAM": { - "id": 20, - "input_subworkflow_step_id": 1, - "output_name": "mapped_reads" - }, - "STAR log": { - "id": 20, - "input_subworkflow_step_id": 0, - "output_name": "output_log" - } - }, - "inputs": [ - { - "description": "", - "name": "Generate Coverage of Unstranded library" - } - ], - "label": "Generate Coverage of Unstranded library", - "name": "Get Uniquely mapped unstranded coverage", - "outputs": [], - "position": { - "left": 2355.0937488734303, - "top": 0 - }, - "subworkflow": { - "a_galaxy_workflow": "true", - "annotation": "", - "comments": [], - "creator": [ - { - "class": "Person", - "identifier": "0000-0002-1964-4960", - "name": "Lucille Delisle" - } - ], - "format-version": "0.1", - "license": "MIT", - "name": "Get Uniquely mapped unstranded coverage", - "report": { - "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" - 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"output_name": "out_file1" - }, - "HideDatasetActionout_file2": { - "action_arguments": {}, - "action_type": "HideDatasetAction", - "output_name": "out_file2" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy2", - "tool_shed_repository": { - "changeset_revision": "993b19f20c76", - "name": "bamtools_filter", - "owner": "devteam", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"conditions\": [{\"__index__\": 0, \"filters\": [{\"__index__\": 0, \"bam_property\": {\"bam_property_selector\": \"tag\", \"__current_case__\": 21, \"bam_property_value\": \"NH=1\"}}]}], \"input_bam\": {\"__class__\": \"ConnectedValue\"}, \"rule_configuration\": {\"rules_selector\": \"false\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.5.2+galaxy2", - "type": "tool", - "uuid": "59db7088-85bf-42ba-9dcd-76836f9d6310", - "when": null, - "workflow_outputs": [] - }, - "4": { - "annotation": "", - 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"tool_state": "{\"d\": false, \"dz\": false, \"five\": false, \"input_type\": {\"input_type_select\": \"bam\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"report\": {\"report_select\": \"bg\", \"__current_case__\": 0, \"zero_regions\": false, \"scale\": {\"__class__\": \"ConnectedValue\"}}, \"split\": true, \"strand\": \"\", \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.31.1", - "type": "tool", - "uuid": "df53e789-be2d-4b09-be8d-a07a35c14913", - "when": null, - "workflow_outputs": [] - }, - "6": { - "annotation": "", - "content_id": "wig_to_bigWig", - "errors": null, - "id": 6, - "input_connections": { - "input1": { - "id": 5, - "output_name": "output" - } - }, - "inputs": [], - "label": "convert both strands coverage to bigwig", - "name": "Wig/BedGraph-to-bigWig", - "outputs": [ - { - "name": "out_file1", - "type": "bigwig" - } - ], - "position": { - "left": 1120, - "top": 67 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "Both Strands Coverage" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } - }, - "tool_id": "wig_to_bigWig", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"settings\": {\"settingsType\": \"preset\", \"__current_case__\": 0}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.1", - "type": "tool", - "uuid": "62d76728-f614-48c0-9560-3abd05b8366d", - "when": null, - "workflow_outputs": [ - { - "label": "Both Strands Coverage", - "output_name": "out_file1", - "uuid": "73763ad9-c132-4764-ada6-eece0c30e74f" - } - ] - } - }, - "tags": [], - "uuid": "451bba09-1c21-4978-b693-4e64402c5787" - }, - "tool_id": null, - "type": "subworkflow", - "uuid": "c46207a6-d625-4646-a72b-79dc2065044f", - "when": null, - "workflow_outputs": [ - { - "label": "Coverage of Unstranded library", - "output_name": "Both Strands Coverage", - "uuid": "8376f1dd-6c9e-4328-a6f1-ebed29f235ff" - 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"version": 55 + "uuid": "894178bf-ba5b-4ad8-afe7-2dbf45557178", + "version": 56 } \ No newline at end of file From 865c0efaaa6b37d35657057ec90f9d1cdb0b0de9 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 18 Oct 2024 16:37:12 +0200 Subject: [PATCH 23/47] make dummy featurecounts as list and remove multiqc wf --- .../rnaseq-pe/rnaseq-pe-tests.yml | 55 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1330 ++++++++++++++--- 2 files changed, 1194 insertions(+), 191 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 1c81a363e..4f8beabf0 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -52,7 +52,6 @@ - class: File identifier: reverse location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger - Generate QC reports?: true Reference genome: dm6 Use featureCounts for generating count tables: true strandedness: unstranded @@ -88,6 +87,24 @@ asserts: has_text: text: "FBgn0017545\t5943" + Coverage of Unstranded library: + element_tests: + GSM461177: + has_size: + value: 445281 + delta: 20000 + GSM461178: + has_size: + value: 406443 + delta: 20000 + GSM461180: + has_size: + value: 423518 + delta: 20000 + GSM461181: + has_size: + value: 455334 + delta: 20000 Mapped Reads: element_tests: GSM461177: @@ -141,4 +158,38 @@ GSM461181: asserts: has_text: - text: "Assigned\t44734" \ No newline at end of file + text: "Assigned\t44734" + Coverage of Stranded libray: + element_tests: + GSM461177_forward: + has_size: + value: 313382 + delta: 15000 + GSM461178_forward: + has_size: + value: 285608 + delta: 15000 + GSM461180_forward: + has_size: + value: 295650 + delta: 15000 + GSM461181_forward: + has_size: + value: 3075214 + delta: 15000 + GSM461177_reverse: + has_size: + value: 313241 + delta: 15000 + GSM461178_reverse: + has_size: + value: 281153 + delta: 15000 + GSM461180_reverse: + has_size: + value: 292239 + delta: 15000 + GSM461181_reverse: + has_size: + value: 322248 + delta: 15000 diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index fd832843a..7962bb8f1 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -13,10 +13,10 @@ "data": { "title": "Map Strandedness parameter" }, - "id": 0, + "id": 1, "position": [ 620.6, - 799.4609386533648 + 1211.9458406962506 ], "size": [ 252.5, @@ -27,21 +27,21 @@ { "child_steps": [ 22, - 25, - 26, + 27, + 28, 21, + 20, 18, - 7, - 19 + 13 ], "color": "turquoise", "data": { "title": "Count table processing" }, - "id": 1, + "id": 0, "position": [ 1001.6, - 429.06093865336476 + 841.5458406962506 ], "size": [ 1268, @@ -86,7 +86,7 @@ "outputs": [], "position": { "left": 0, - "top": 420.7131881663027 + "top": 833.1980902091885 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -97,37 +97,10 @@ "workflow_outputs": [] }, "1": { - "annotation": "Whether to report QC", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "Whether to report QC", - "name": "Generate QC reports?" - } - ], - "label": "Generate QC reports?", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 40, - "top": 530.7131881663026 - }, - "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "f3dcb910-684b-463d-bf98-03bc18451666", - "when": null, - "workflow_outputs": [] - }, - "2": { "annotation": "Select the reference genome", "content_id": null, "errors": null, - "id": 2, + "id": 1, "input_connections": {}, "inputs": [ { @@ -140,7 +113,7 @@ "outputs": [], "position": { "left": 69.99997051198416, - "top": 642.348891387906 + "top": 1054.8337934307917 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -150,11 +123,11 @@ "when": null, "workflow_outputs": [] }, - "3": { + "2": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, - "id": 3, + "id": 2, "input_connections": {}, "inputs": [ { @@ -167,7 +140,7 @@ "outputs": [], "position": { "left": 119.99999475982484, - "top": 739.5207231178792 + "top": 1152.005625160765 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -177,11 +150,11 @@ "when": null, "workflow_outputs": [] }, - "4": { + "3": { "annotation": "Use featureCounts tool instead of RNA STAR?", "content_id": null, "errors": null, - "id": 4, + "id": 3, "input_connections": {}, "inputs": [ { @@ -194,7 +167,7 @@ "outputs": [], "position": { "left": 159.66015029117847, - "top": 848.2541246418339 + "top": 1260.7390266847196 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -204,6 +177,40 @@ "when": null, "workflow_outputs": [] }, + "4": { + "annotation": "This file will be used in MultiQC if the user opts out of featureCounts to generate count files. 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"annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", "errors": null, - "id": 23, + "id": 25, "input_connections": { "guide|guide_source|ref_hist": { - "id": 3, + "id": 2, "output_name": "output" }, "input_options|input_bam": { - "id": 20, + "id": 19, "output_name": "mapped_reads" }, "rna_strandness": { @@ -1043,7 +1995,7 @@ "output_name": "output_param_text" }, "when": { - "id": 9, + "id": 8, "output_name": "output" } }, @@ -1071,7 +2023,7 @@ ], "position": { "left": 2386.0764558032492, - "top": 1151.897928923608 + "top": 1564.3828309664939 }, "post_job_actions": { "HideDatasetActionoutput_gtf": { @@ -1107,30 +2059,30 @@ } ] }, - "24": { + "26": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", "errors": null, - "id": 24, + "id": 26, "input_connections": { "advanced_settings|library_type": { "id": 15, "output_name": "output_param_text" }, "advanced_settings|mask_file": { - "id": 8, + "id": 7, "output_name": "output" }, "bias_correction|seq_source|index": { - "id": 13, + "id": 12, "output_name": "out1" }, "input": { - "id": 20, + "id": 19, "output_name": "mapped_reads" }, "reference_annotation|reference_annotation_file": { - "id": 3, + "id": 2, "output_name": "output" }, "when": { @@ -1178,7 +2130,7 @@ ], "position": { "left": 2396.799924469628, - "top": 1534.4695573077954 + "top": 1946.9544593506812 }, "post_job_actions": { "HideDatasetActionassembled_isoforms": { @@ -1236,18 +2188,18 @@ } ] }, - "25": { + "27": { "annotation": "featureCounts summaries", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 25, + "id": 27, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 21, "output_name": "output_summary" }, "style_cond|type_cond|pick_from_1|value": { - "id": 18, + "id": 20, "output_name": "output" } }, @@ -1261,8 +2213,8 @@ } ], "position": { - "left": 2049.6016957581687, - "top": 516.3680489231292 + "left": 2047.540257415934, + "top": 930.8972239041321 }, "post_job_actions": { "RenameDatasetActiondata_param": { @@ -1293,11 +2245,11 @@ } ] }, - "26": { + "28": { "annotation": "Counts Table ", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 26, + "id": 28, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 21, @@ -1319,7 +2271,7 @@ ], "position": { "left": 1772.09442258672, - "top": 776.9993966536306 + "top": 1189.4842986965164 }, "post_job_actions": { "RenameDatasetActiondata_param": { @@ -1350,18 +2302,18 @@ } ] }, - "27": { + "29": { "annotation": "", "content_id": "__TAG_FROM_FILE__", "errors": null, - "id": 27, + "id": 29, "input_connections": { "input": { - "id": 26, + "id": 28, "output_name": "data_param" }, "tags": { - "id": 19, + "id": 18, "output_name": "outfile" } }, @@ -1376,7 +2328,7 @@ ], "position": { "left": 2074.833052722927, - "top": 833.4952833657751 + "top": 1245.9801854086609 }, "post_job_actions": {}, "tool_id": "__TAG_FROM_FILE__", @@ -1387,22 +2339,22 @@ "when": null, "workflow_outputs": [] }, - "28": { + "30": { "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "errors": null, - "id": 28, + "id": 30, "input_connections": { "batch_factors": { - "id": 11, + "id": 10, "output_name": "output" }, "header": { - "id": 4, + "id": 3, "output_name": "output" }, "select_data|countsFile": { - "id": 27, + "id": 29, "output_name": "output" } }, @@ -1426,7 +2378,7 @@ ], "position": { "left": 2396.1152868376967, - "top": 616.438044904801 + "top": 1028.9229469476868 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -1473,6 +2425,6 @@ "tags": [ "RNAseq" ], - "uuid": "894178bf-ba5b-4ad8-afe7-2dbf45557178", - "version": 56 + "uuid": "ec8e2ed5-bef3-4bf2-9fe3-b6316a9aa415", + "version": 59 } \ No newline at end of file From bb6c038a2671e95780eab91dca1cc8dc705a10f6 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 18 Oct 2024 17:33:23 +0200 Subject: [PATCH 24/47] without featurecounts summary and stranded coverage --- .../rnaseq-pe/rnaseq-pe-tests.yml | 54 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1060 +++-------------- 2 files changed, 155 insertions(+), 959 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 4f8beabf0..f7c37ac85 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -140,56 +140,4 @@ GSM461181: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" - FeatureCounts Summary Table: - element_tests: - GSM461177: - asserts: - has_text: - text: "Assigned\t45715" - GSM461178: - asserts: - has_text: - text: "Assigned\t38738" - GSM461180: - asserts: - has_text: - text: "Assigned\t39998" - GSM461181: - asserts: - has_text: - text: "Assigned\t44734" - Coverage of Stranded libray: - element_tests: - GSM461177_forward: - has_size: - value: 313382 - delta: 15000 - GSM461178_forward: - has_size: - value: 285608 - delta: 15000 - GSM461180_forward: - has_size: - value: 295650 - delta: 15000 - GSM461181_forward: - has_size: - value: 3075214 - delta: 15000 - GSM461177_reverse: - has_size: - value: 313241 - delta: 15000 - GSM461178_reverse: - has_size: - value: 281153 - delta: 15000 - GSM461180_reverse: - has_size: - value: 292239 - delta: 15000 - GSM461181_reverse: - has_size: - value: 322248 - delta: 15000 + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 7962bb8f1..1b89fcd80 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -4,48 +4,45 @@ "comments": [ { "child_steps": [ - 14, - 15, - 16, - 17 + 19, + 23, + 18, + 16 ], - "color": "lime", + "color": "turquoise", "data": { - "title": "Map Strandedness parameter" + "title": "Count table processing" }, "id": 1, "position": [ - 620.6, - 1211.9458406962506 + 1001.6, + 429.06093865336476 ], "size": [ - 252.5, - 728.6 + 1268, + 696 ], "type": "frame" }, { "child_steps": [ - 22, - 27, - 28, - 21, - 20, - 18, - 13 + 12, + 13, + 14, + 15 ], - "color": "turquoise", + "color": "lime", "data": { - "title": "Count table processing" + "title": "Map Strandedness parameter" }, "id": 0, "position": [ - 1001.6, - 841.5458406962506 + 620.6, + 799.4609386533648 ], "size": [ - 1268, - 696 + 252.5, + 728.6 ], "type": "frame" } @@ -64,6 +61,7 @@ ], "format-version": "0.1", "license": "MIT", + "release": "0.10", "name": "RNAseq_PE", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" @@ -86,7 +84,7 @@ "outputs": [], "position": { "left": 0, - "top": 833.1980902091885 + "top": 420.7131881663027 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -113,7 +111,7 @@ "outputs": [], "position": { "left": 69.99997051198416, - "top": 1054.8337934307917 + "top": 642.348891387906 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -140,7 +138,7 @@ "outputs": [], "position": { "left": 119.99999475982484, - "top": 1152.005625160765 + "top": 739.5207231178792 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -167,7 +165,7 @@ "outputs": [], "position": { "left": 159.66015029117847, - "top": 1260.7390266847196 + "top": 848.2541246418339 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -178,44 +176,10 @@ "workflow_outputs": [] }, "4": { - "annotation": "This file will be used in MultiQC if the user opts out of featureCounts to generate count files. ", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", - "errors": null, - "id": 4, - "input_connections": {}, - "inputs": [], - "label": "A dummy featureCounts summary file", - "name": "Create text file", - "outputs": [ - { - "name": "outfile", - "type": "txt" - } - ], - "position": { - "left": 726.2294178036034, - "top": 1056.4566869511411 - }, - "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", - "tool_shed_repository": { - "changeset_revision": "86755160afbf", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"token_set\": [{\"__index__\": 0, \"line\": \"Status\\tFeaturecounts_was_not_used\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}, {\"__index__\": 1, \"line\": \"Assigned\\t0\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}, {\"__index__\": 2, \"line\": \"Unassigned_Unmapped\\t0\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"1\"}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "9.3+galaxy1", - "type": "tool", - "uuid": "be0268be-a3ec-4d75-854b-d8eecf4b4521", - "when": null, - "workflow_outputs": [] - }, - "5": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, - "id": 5, + "id": 4, "input_connections": {}, "inputs": [ { @@ -228,7 +192,7 @@ "outputs": [], "position": { "left": 203.2055169930919, - "top": 1396.390999469709 + "top": 983.9060974268232 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -238,11 +202,11 @@ "when": null, "workflow_outputs": [] }, - "6": { + "5": { "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, - "id": 6, + "id": 5, "input_connections": {}, "inputs": [ { @@ -255,7 +219,7 @@ "outputs": [], "position": { "left": 228.09439688484417, - "top": 1491.5304593353903 + "top": 1079.0455572925046 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -265,11 +229,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "6": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 7, + "id": 6, "input_connections": {}, "inputs": [ { @@ -282,7 +246,7 @@ "outputs": [], "position": { "left": 259.4363655681731, - "top": 1609.8186191969191 + "top": 1197.3337171540334 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -292,11 +256,11 @@ "when": null, "workflow_outputs": [] }, - "8": { + "7": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 8, + "id": 7, "input_connections": {}, "inputs": [ { @@ -309,7 +273,7 @@ "outputs": [], "position": { "left": 268.103514973962, - "top": 1731.006044517324 + "top": 1318.5211424744382 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -319,11 +283,11 @@ "when": null, "workflow_outputs": [] }, - "9": { + "8": { "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. 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"29": { + "24": { "annotation": "", "content_id": "__TAG_FROM_FILE__", "errors": null, - "id": 29, + "id": 24, "input_connections": { "input": { - "id": 28, + "id": 23, "output_name": "data_param" }, "tags": { - "id": 18, + "id": 16, "output_name": "outfile" } }, @@ -2328,7 +1576,7 @@ ], "position": { "left": 2074.833052722927, - "top": 1245.9801854086609 + "top": 833.4952833657751 }, "post_job_actions": {}, "tool_id": "__TAG_FROM_FILE__", @@ -2339,14 +1587,14 @@ "when": null, "workflow_outputs": [] }, - "30": { + "25": { "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "errors": null, - "id": 30, + "id": 25, "input_connections": { "batch_factors": { - "id": 10, + "id": 9, "output_name": "output" }, "header": { @@ -2354,7 +1602,7 @@ "output_name": "output" }, "select_data|countsFile": { - "id": 29, + "id": 24, "output_name": "output" } }, @@ -2378,7 +1626,7 @@ ], "position": { "left": 2396.1152868376967, - "top": 1028.9229469476868 + "top": 616.438044904801 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -2425,6 +1673,6 @@ "tags": [ "RNAseq" ], - "uuid": "ec8e2ed5-bef3-4bf2-9fe3-b6316a9aa415", - "version": 59 + "uuid": "05594672-3de3-432f-a894-3953282bde2d", + "version": 60 } \ No newline at end of file From 1b9c7066f72802a2662b38c1ee8c8510fbf1f490 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 21 Oct 2024 16:45:16 +0200 Subject: [PATCH 25/47] move count table processing to a subworkflow so that it can be used in single-end workflow --- .../rnaseq-pe/rnaseq-pe-tests.yml | 174 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 2821 +++++++++++++---- 2 files changed, 2421 insertions(+), 574 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index f7c37ac85..a932e5f22 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -1,4 +1,4 @@ -- doc: Test outline for RNAseq_PE +- doc: Test outline for rnaseq-pe job: GTF file of annotation: class: File @@ -6,7 +6,7 @@ filetype: gtf Sample table: class: File - location: https://zenodo.org/records/13951092/files//Sample_table.tabular + location: https://zenodo.org/records/13951092/files/Sample_table.tabular filetype: tabular Collection paired FASTQ files: class: Collection @@ -52,42 +52,124 @@ - class: File identifier: reverse location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger + Generate QC reports?: true Reference genome: dm6 Use featureCounts for generating count tables: true strandedness: unstranded - Compute Cufflinks FPKM?: false + Compute Cufflinks FPKM?: true GTF with regions to exclude from FPKM normalization with Cufflinks: null Compute StringTie FPKM?: true DEseq2 batch factors: null outputs: + DESeq2 Plots: + has_size: + size: 33420 + delta: 1500 Differential Expression Analysis using DESeq2: asserts: has_text_matching: expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" - DESeq2 Plots: - has_size: - size: 33420 - delta: 1500 - Counts Table: + MultiQC stats: + asserts: + has_text_matching: + expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*" + expression: "GSM461177_forward\t\t\t\t\t\t\t\t\t\t\t27.95[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" + expression: "GSM461177_reverse\t\t\t\t\t\t\t\t\t\t\t28.22[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" + expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" + expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + + Mapped Reads: + element_tests: + GSM461177: + has_size: + value: 3058282 + delta: 150000 + GSM461178: + has_size: + value: 3032322 + delta: 150000 + GSM461180: + has_size: + value: 3165439 + delta: 150000 + GSM461181: + has_size: + value: 3075214 + delta: 150000 + + Genes Expression from Cufflinks: + element_tests: + GSM461177: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + GSM461178: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 141422 134823 148020 OK" + GSM461180: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 134779 128494 141063 OK" + GSM461181: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 127880 121988 133772 OK" + Transcripts Expression from Cufflinks: element_tests: GSM461177: asserts: - has_text: - text: "FBgn0017545\t6109" + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" GSM461178: asserts: - has_text: - text: "FBgn0017545\t5649" + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 370.382 128757 122145 135370 OK" GSM461180: asserts: - has_text: - text: "FBgn0017545\t5600" + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 366.172 122426 116120 128732 OK" GSM461181: asserts: - has_text: - text: "FBgn0017545\t5943" - Coverage of Unstranded library: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" + Stranded Coverage: + element_tests: + GSM461177_forward: + has_size: + value: 313382 + delta: 15000 + GSM461178_forward: + has_size: + value: 285608 + delta: 15000 + GSM461180_forward: + has_size: + value: 295650 + delta: 15000 + GSM461181_forward: + has_size: + value: 311698 + delta: 15000 + GSM461177_reverse: + has_size: + value: 313241 + delta: 15000 + GSM461178_reverse: + has_size: + value: 281153 + delta: 15000 + GSM461180_reverse: + has_size: + value: 292239 + delta: 15000 + GSM461181_reverse: + has_size: + value: 322248 + delta: 15000 + Unstranded Coverage: element_tests: GSM461177: has_size: @@ -105,24 +187,6 @@ has_size: value: 455334 delta: 20000 - Mapped Reads: - element_tests: - GSM461177: - has_size: - value: 3058282 - delta: 150000 - GSM461178: - has_size: - value: 3032322 - delta: 150000 - GSM461180: - has_size: - value: 3165439 - delta: 150000 - GSM461181: - has_size: - value: 3075214 - delta: 150000 Gene Abundance Estimates from StringTie: element_tests: GSM461177: @@ -140,4 +204,42 @@ GSM461181: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" \ No newline at end of file + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" + + Tagged Count Tables: + element_tests: + GSM461177: + asserts: + has_line: + line: "FBgn0017545 6109" + GSM461178: + asserts: + has_line: + line: "FBgn0017545 5649" + GSM461180: + asserts: + has_line: + line: "FBgn0017545 5600" + GSM461181: + asserts: + has_line: + line: "FBgn0017545 5943" + + FeatureCounts Summary Table: + element_tests: + GSM461177: + asserts: + has_line: + line: "Assigned 45715" + GSM461178: + asserts: + has_line: + line: "Assigned 38738" + GSM461180: + asserts: + has_line: + line: "Assigned 39998" + GSM461181: + asserts: + has_line: + line: "Assigned 44734" diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 1b89fcd80..7101f0647 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -4,32 +4,29 @@ "comments": [ { "child_steps": [ - 19, - 23, - 18, - 16 + 21, + 22 ], - "color": "turquoise", + "color": "red", "data": { - "title": "Count table processing" + "title": "Coverage Files" }, - "id": 1, + "id": 2, "position": [ - 1001.6, - 429.06093865336476 + 2510.1, + 0 ], "size": [ - 1268, - 696 + 375, + 538 ], "type": "frame" }, { "child_steps": [ - 12, - 13, 14, - 15 + 15, + 16 ], "color": "lime", "data": { @@ -37,12 +34,33 @@ }, "id": 0, "position": [ - 620.6, - 799.4609386533648 + 770.5, + 1592.6 + ], + "size": [ + 251, + 558 + ], + "type": "frame" + }, + { + "child_steps": [ + 13, + 19, + 20 + ], + "color": "yellow", + "data": { + "title": "Additional quantification" + }, + "id": 1, + "position": [ + 1306.2, + 1413.8 ], "size": [ - 252.5, - 728.6 + 860, + 716 ], "type": "frame" } @@ -62,7 +80,7 @@ "format-version": "0.1", "license": "MIT", "release": "0.10", - "name": "RNAseq_PE", + "name": "rnaseq-pe", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -84,22 +102,55 @@ "outputs": [], "position": { "left": 0, - "top": 420.7131881663027 + "top": 1007.0008028213834 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "b6379949-1974-4250-b476-dee789f918db", + "uuid": "020f7580-f647-471f-b210-dbf9dfcf80bf", "when": null, "workflow_outputs": [] }, "1": { - "annotation": "Select the reference genome", + "annotation": "Whether to report QC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, + "inputs": [ + { + "description": "Whether to report QC", + "name": "Generate QC reports?" + } + ], + "label": "Generate QC reports?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40.67737161137343, + "top": 1117.6931018245803 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "bea331ce-d6fa-4312-8dce-a8b13bc4e77b", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d9ae5b99-709d-4a01-8b07-216de631e3d4" + } + ] + }, + "2": { + "annotation": "Select the reference genome", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, "inputs": [ { "description": "Select the reference genome", @@ -110,22 +161,28 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 69.99997051198416, - "top": 642.348891387906 + "left": 70.67734212335759, + "top": 1229.3288050461836 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", + "uuid": "a72b29ae-65a7-4e4d-a996-2943ab5b02aa", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "29c5e09e-8144-45dc-aa55-8c767349c508" + } + ] }, - "2": { + "3": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, - "id": 2, + "id": 3, "input_connections": {}, "inputs": [ { @@ -137,22 +194,22 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 119.99999475982484, - "top": 739.5207231178792 + "left": 120.67736637119827, + "top": 1326.5006367761569 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", "tool_version": null, "type": "data_input", - "uuid": "423b33a8-0778-46a5-b5fb-2a8199660076", + "uuid": "4987fd01-b72c-4bc0-9d49-a840a0d04b8e", "when": null, "workflow_outputs": [] }, - "3": { + "4": { "annotation": "Use featureCounts tool instead of RNA STAR?", "content_id": null, "errors": null, - "id": 3, + "id": 4, "input_connections": {}, "inputs": [ { @@ -164,22 +221,28 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 159.66015029117847, - "top": 848.2541246418339 + "left": 160.33752190255188, + "top": 1435.2340383001115 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "8775ddf1-48f2-423e-813a-b5d302888580", + "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "e65f5234-ab27-4b06-a4c4-5178cf3f32f0" + } + ] }, - "4": { + "5": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, - "id": 4, + "id": 5, "input_connections": {}, "inputs": [ { @@ -191,22 +254,28 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 203.2055169930919, - "top": 983.9060974268232 + "left": 203.8828886044653, + "top": 1570.8860110851008 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "180fc8bd-b8f4-486b-b300-e503bf379373", + "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "24881e16-6148-442f-ace3-bc99670d6e21" + } + ] }, - "5": { + "6": { "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, - "id": 5, + "id": 6, "input_connections": {}, "inputs": [ { @@ -218,103 +287,121 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 228.09439688484417, - "top": 1079.0455572925046 + "left": 228.7717684962176, + "top": 1666.0254709507822 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "35a99e85-127a-48b1-80fb-30d6b08aff92", + "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "a6d6516a-3881-4b6f-b94d-ed5709c53fe3" + } + ] }, - "6": { - "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", + "7": { + "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", "content_id": null, "errors": null, - "id": 6, + "id": 7, "input_connections": {}, "inputs": [ { - "description": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", - "name": "GTF with regions to exclude from FPKM normalization with Cufflinks" + "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "name": "Sample table" } ], - "label": "GTF with regions to exclude from FPKM normalization with Cufflinks", + "label": "Sample table", "name": "Input dataset", "outputs": [], "position": { - "left": 259.4363655681731, - "top": 1197.3337171540334 + "left": 1462.1645523806205, + "top": 909.2581294996864 }, "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": \"\"}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "1d1b3d41-0efa-4ffa-aba9-0e80a51173a5", + "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", "when": null, "workflow_outputs": [] }, - "7": { - "annotation": "Whether FPKM values should be computed with StringTie", + "8": { + "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 7, + "id": 8, "input_connections": {}, "inputs": [ { - "description": "Whether FPKM values should be computed with StringTie", - "name": "Compute StringTie FPKM?" + "description": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", + "name": "GTF with regions to exclude from FPKM normalization with Cufflinks" } ], - "label": "Compute StringTie FPKM?", - "name": "Input parameter", + "label": "GTF with regions to exclude from FPKM normalization with Cufflinks", + "name": "Input dataset", "outputs": [], "position": { - "left": 268.103514973962, - "top": 1318.5211424744382 + "left": 260.1137371795465, + "top": 1784.313630812311 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"optional\": true, \"tag\": \"\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "47972cba-6df9-4883-8280-24ea28bcc4bb", + "type": "data_input", + "uuid": "0d4e1623-adc9-4ff3-8156-7e1322b1e278", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c4058f91-dda0-4063-beaa-33505d1754d1" + } + ] }, - "8": { - "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "9": { + "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 8, + "id": 9, "input_connections": {}, "inputs": [ { - "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "name": "Sample table" + "description": "Whether FPKM values should be computed with StringTie", + "name": "Compute StringTie FPKM?" } ], - "label": "Sample table", - "name": "Input dataset", + "label": "Compute StringTie FPKM?", + "name": "Input parameter", "outputs": [], "position": { - "left": 271.9528882100886, - "top": 1413.283953646225 + "left": 268.7808865853354, + "top": 1905.5010561327158 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, - "type": "data_input", - "uuid": "9b903f17-a37b-48d9-a214-bcdf393a7574", + "type": "parameter_input", + "uuid": "056f11f4-bdd9-4361-b037-2c0822320cc2", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "51b56f88-8607-4fc5-b958-19bd1ca31901" + } + ] }, - "9": { + "10": { "annotation": "Tabular file with additional batch factors to include in the model", "content_id": null, "errors": null, - "id": 9, + "id": 10, "input_connections": {}, "inputs": [ { @@ -326,22 +413,28 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 1906.3299807760093, - "top": 1229.860451672463 + "left": 2203.102316887585, + "top": 1355.0225413410844 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": null}", "tool_version": null, "type": "data_input", - "uuid": "96d02185-64bb-4d77-b986-cc6209329334", + "uuid": "6abd6f58-1f0a-477c-9783-6f8dcfafb77d", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "c1ac1a43-8bb1-44d4-8f88-540cb2ab7852" + } + ] }, - "10": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 10, + "id": 11, "input_connections": { "library|input_1": { "id": 0, @@ -367,8 +460,8 @@ } ], "position": { - "left": 310.957760903539, - "top": 243.76174078998673 + "left": 239.35765144976227, + "top": 494.46848655874044 }, "post_job_actions": { "HideDatasetActionout1": { @@ -397,18 +490,51 @@ "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "4.9+galaxy1", "type": "tool", - "uuid": "bb78142b-c185-40a6-b7c5-4fa9f6b3d314", + "uuid": "86b5b52b-cf40-4d34-9b60-7ede0e187b4f", "when": null, "workflow_outputs": [] }, - "11": { + "12": { + "annotation": "", + "content_id": "__FLATTEN__", + "errors": null, + "id": 12, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Flatten collection", + "outputs": [ + { + "name": "output", + "type": "input" + } + ], + "position": { + "left": 345.7624932537463, + "top": 963.9873433527641 + }, + "post_job_actions": {}, + "tool_id": "__FLATTEN__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"join_identifier\": \"_\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "dddbd652-fe4f-42c8-a2ff-bdc259d4928c", + "when": null, + "workflow_outputs": [] + }, + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 11, + "id": 13, "input_connections": { "components_0|param_type|component_value": { - "id": 1, + "id": 2, "output_name": "output" } }, @@ -422,8 +548,8 @@ } ], "position": { - "left": 785.2116386388172, - "top": 1651.2722585317363 + "left": 1412.7865078407585, + "top": 1513.204961480357 }, "post_job_actions": { "HideDatasetActionout1": { @@ -442,18 +568,18 @@ "tool_state": "{\"components\": [{\"__index__\": 0, \"param_type\": {\"select_param_type\": \"text\", \"__current_case__\": 0, \"component_value\": {\"__class__\": \"ConnectedValue\"}}}], \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.1", "type": "tool", - "uuid": "7439bab2-1fb4-46e9-974f-b2ad7171f273", + "uuid": "bcceb886-0592-4b3f-8b39-26fe79caeb62", "when": null, "workflow_outputs": [] }, - "12": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 12, + "id": 14, "input_connections": { "input_param_type|input_param": { - "id": 4, + "id": 5, "output_name": "output" } }, @@ -472,8 +598,8 @@ } ], "position": { - "left": 653.0727821873274, - "top": 839.4226289581652 + "left": 795.1082525210539, + "top": 1643.2637555172578 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -492,18 +618,18 @@ "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - forward\", \"to\": \"1\"}, {\"__index__\": 1, \"from\": \"stranded - reverse\", \"to\": \"2\"}, {\"__index__\": 2, \"from\": \"unstranded\", \"to\": \"0\"}]}, \"output_param_type\": \"text\", \"unmapped\": {\"on_unmapped\": \"fail\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.2.0", "type": "tool", - "uuid": "a8136f44-5f46-44eb-bfdd-4fbb670493e0", + "uuid": "72d7d4d1-d1be-481c-b2a1-1e85192b2661", "when": null, "workflow_outputs": [] }, - "13": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 13, + "id": 15, "input_connections": { "input_param_type|input_param": { - "id": 4, + "id": 5, 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"input_connections": { "batch_factors": { - "id": 9, + "id": 10, "output_name": "output" }, "header": { - "id": 3, + "id": 4, "output_name": "output" }, "select_data|countsFile": { - "id": 24, - "output_name": "output" + "id": 23, + "output_name": "Tagged Count Tables" } }, "inputs": [ @@ -1625,8 +3370,8 @@ } ], "position": { - "left": 2396.1152868376967, - "top": 616.438044904801 + "left": 2566.26663539139, + "top": 1017.2514257011151 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -1654,18 +3399,18 @@ "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"ConnectedValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", 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"uuid": "fba8ce87-d322-44b3-a217-53f6a1455225" + "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" } ] } @@ -1673,6 +3418,6 @@ "tags": [ "RNAseq" ], - "uuid": "05594672-3de3-432f-a894-3953282bde2d", - "version": 60 + "uuid": "9d7f7cff-dbd4-4f0b-a87f-8ab256cd0776", + "version": 9 } \ No newline at end of file From d7e53d43811375f214071b3c8a8d9ad4de57d63d Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 21 Oct 2024 17:53:12 +0200 Subject: [PATCH 26/47] remove coverage subworkflows --- .../rnaseq-pe/rnaseq-pe-tests.yml | 56 - .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1495 +++-------------- 2 files changed, 262 insertions(+), 1289 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index a932e5f22..b5cbbfa4a 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -79,7 +79,6 @@ expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" - Mapped Reads: element_tests: GSM461177: @@ -98,7 +97,6 @@ has_size: value: 3075214 delta: 150000 - Genes Expression from Cufflinks: element_tests: GSM461177: @@ -135,58 +133,6 @@ asserts: has_line: line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" - Stranded Coverage: - element_tests: - GSM461177_forward: - has_size: - value: 313382 - delta: 15000 - GSM461178_forward: - has_size: - value: 285608 - delta: 15000 - GSM461180_forward: - has_size: - value: 295650 - delta: 15000 - GSM461181_forward: - has_size: - value: 311698 - delta: 15000 - GSM461177_reverse: - has_size: - value: 313241 - delta: 15000 - GSM461178_reverse: - has_size: - value: 281153 - delta: 15000 - GSM461180_reverse: - has_size: - value: 292239 - delta: 15000 - GSM461181_reverse: - has_size: - value: 322248 - delta: 15000 - Unstranded Coverage: - element_tests: - GSM461177: - has_size: - value: 445281 - delta: 20000 - GSM461178: - has_size: - value: 406443 - delta: 20000 - GSM461180: - has_size: - value: 423518 - delta: 20000 - GSM461181: - has_size: - value: 455334 - delta: 20000 Gene Abundance Estimates from StringTie: element_tests: GSM461177: @@ -205,7 +151,6 @@ asserts: has_text_matching: expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" - Tagged Count Tables: element_tests: GSM461177: @@ -224,7 +169,6 @@ asserts: has_line: line: "FBgn0017545 5943" - FeatureCounts Summary Table: element_tests: GSM461177: diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 7101f0647..608fd6de1 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -4,21 +4,22 @@ "comments": [ { "child_steps": [ - 21, - 22 + 13, + 19, + 20 ], - "color": "red", + "color": "yellow", "data": { - "title": "Coverage Files" + "title": "Additional quantification" }, - "id": 2, + "id": 1, "position": [ - 2510.1, - 0 + 1306.2, + 919.3315134412595 ], "size": [ - 375, - 538 + 860, + 716 ], "type": "frame" }, @@ -35,34 +36,13 @@ "id": 0, "position": [ 770.5, - 1592.6 + 1098.1315134412594 ], "size": [ 251, 558 ], "type": "frame" - }, - { - "child_steps": [ - 13, - 19, - 20 - ], - "color": "yellow", - "data": { - "title": "Additional quantification" - }, - "id": 1, - "position": [ - 1306.2, - 1413.8 - ], - "size": [ - 860, - 716 - ], - "type": "frame" } ], "creator": [ @@ -102,7 +82,7 @@ "outputs": [], "position": { "left": 0, - "top": 1007.0008028213834 + "top": 512.532316262643 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -129,7 +109,7 @@ "outputs": [], "position": { "left": 40.67737161137343, - "top": 1117.6931018245803 + "top": 623.2246152658398 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -141,7 +121,7 @@ { "label": null, "output_name": "output", - "uuid": "d9ae5b99-709d-4a01-8b07-216de631e3d4" + "uuid": "c1ce73d9-f523-4d63-a52a-039977774544" } ] }, @@ -162,7 +142,7 @@ "outputs": [], "position": { "left": 70.67734212335759, - "top": 1229.3288050461836 + "top": 734.8603184874431 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -174,7 +154,7 @@ { "label": null, "output_name": "output", - "uuid": "29c5e09e-8144-45dc-aa55-8c767349c508" + "uuid": "52c139e7-d360-4a4e-b6c7-0c5109d791d8" } ] }, @@ -195,7 +175,7 @@ "outputs": [], "position": { "left": 120.67736637119827, - "top": 1326.5006367761569 + "top": 832.0321502174164 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -222,7 +202,7 @@ "outputs": [], "position": { "left": 160.33752190255188, - "top": 1435.2340383001115 + "top": 940.765551741371 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -234,7 +214,7 @@ { "label": null, "output_name": "output", - "uuid": "e65f5234-ab27-4b06-a4c4-5178cf3f32f0" + "uuid": "455c5109-a8f2-4fb0-baa9-2863ace00a98" } ] }, @@ -255,7 +235,7 @@ "outputs": [], "position": { "left": 203.8828886044653, - "top": 1570.8860110851008 + "top": 1076.4175245263605 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -267,7 +247,7 @@ { "label": null, "output_name": "output", - "uuid": "24881e16-6148-442f-ace3-bc99670d6e21" + "uuid": "5b9b3b69-3ffd-47ce-86ed-1ed8ec45f1f1" } ] }, @@ -288,7 +268,7 @@ "outputs": [], "position": { "left": 228.7717684962176, - 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This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "content_id": null, - "errors": null, - "id": 7, - "input_connections": {}, - "inputs": [ - { - "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "name": "Sample table" - } - ], - "label": "Sample table", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1462.1645523806205, - "top": 909.2581294996864 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", - "when": null, - "workflow_outputs": [] - }, - "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 8, + "id": 7, "input_connections": {}, "inputs": [ { @@ -348,7 +301,7 @@ "outputs": [], "position": { "left": 260.1137371795465, - "top": 1784.313630812311 + "top": 1289.8451442535707 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -360,15 +313,15 @@ { "label": null, "output_name": "output", - "uuid": "c4058f91-dda0-4063-beaa-33505d1754d1" + "uuid": "892a5cac-97a8-4194-9887-463c741590d9" } ] }, - "9": { + "8": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 9, + "id": 8, "input_connections": {}, "inputs": [ { @@ -381,7 +334,7 @@ "outputs": [], "position": { "left": 268.7808865853354, - "top": 1905.5010561327158 + "top": 1411.0325695739753 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -393,10 +346,37 @@ { "label": null, "output_name": "output", - "uuid": "51b56f88-8607-4fc5-b958-19bd1ca31901" + "uuid": "0eb6e8d3-dbb3-486e-b6c2-f7ed2700b5f4" } ] }, + "9": { + "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "content_id": null, + "errors": null, + "id": 9, + "input_connections": {}, + "inputs": [ + { + "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "name": "Sample table" + } + ], + "label": "Sample table", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 1462.1645523806205, + "top": 414.789642940946 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", + "when": null, + "workflow_outputs": [] + }, "10": { "annotation": "Tabular file with additional batch factors to include in the model", "content_id": null, @@ -414,7 +394,7 @@ "outputs": [], "position": { "left": 2203.102316887585, - "top": 1355.0225413410844 + "top": 860.554054782344 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": null}", @@ -426,7 +406,7 @@ { "label": null, "output_name": "output", - "uuid": "c1ac1a43-8bb1-44d4-8f88-540cb2ab7852" + "uuid": "ae3cb027-73f5-41b9-a2e7-2a2fdabd37b7" } ] }, @@ -461,7 +441,7 @@ ], "position": { "left": 239.35765144976227, - 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"label": null, - "output_name": "0:output", - "uuid": "dd4fcfc3-8415-4d1a-b65a-10203ca6ac29" + "label": "Genes Expression from Cufflinks", + "output_name": "genes_expression", + "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" }, { - "label": "Stranded Coverage", - "output_name": "Uniquely Mapped Stranded Coverage", - "uuid": "9161f772-6904-4479-aff4-566295f5b3b2" + "label": "Transcripts Expression from Cufflinks", + "output_name": "transcripts_expression", + "uuid": "2c13ef79-948c-4f5f-8516-a769550128fd" } ] }, - "23": { + "21": { "annotation": "", - "id": 23, + "id": 21, "input_connections": { "RNA STAR count tables": { "id": 17, @@ -2081,7 +1110,7 @@ "output_name": "reads_per_gene" }, "Sample table to add tags": { - "id": 7, + "id": 9, "input_subworkflow_step_id": 2, "output_name": "output" }, @@ -2107,7 +1136,7 @@ "outputs": [], "position": { "left": 1875.6228149071408, - "top": 962.4763887841759 + "top": 468.0079022254355 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2149,7 +1178,7 @@ ], "position": { "left": 2.142187583634133, - "top": 16.0 + "top": 16 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", @@ -2329,7 +1358,7 @@ ], "position": { "left": 282.1421365930926, - "top": 0.0 + "top": 0 }, "post_job_actions": { "ChangeDatatypeActionoutput": { @@ -2469,7 +1498,7 @@ ], "position": { "left": 842.1422267022583, - "top": 16.0 + "top": 16 }, "post_job_actions": { "RenameDatasetActiondata_param": { @@ -2657,7 +1686,7 @@ { "label": null, "output_name": "3:output", - "uuid": "f8d298cc-b2c6-43d7-8904-32f1ec1e7c50" + "uuid": "17690e9c-c087-41b6-a4d2-ec77d82f285f" }, { "label": "FeatureCounts Summary Table", @@ -2671,9 +1700,9 @@ } ] }, - "24": { + "22": { "annotation": "", - "id": 24, + "id": 22, "input_connections": { "Cutadapt Reports": { "id": 11, @@ -2696,7 +1725,7 @@ "output_name": "mapped_reads" }, "featureCounts summaries": { - "id": 23, + "id": 21, "input_subworkflow_step_id": 1, "output_name": "FeatureCounts Summary Table" }, @@ -2721,7 +1750,7 @@ "outputs": [], "position": { "left": 2581.8385293658202, - "top": 574.7767421741249 + "top": 80.3082556153845 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3332,11 +2361,11 @@ } ] }, - "25": { + "23": { "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "errors": null, - "id": 25, + "id": 23, "input_connections": { "batch_factors": { "id": 10, @@ -3347,7 +2376,7 @@ "output_name": "output" }, "select_data|countsFile": { - "id": 23, + "id": 21, "output_name": "Tagged Count Tables" } }, @@ -3371,7 +2400,7 @@ ], "position": { "left": 2566.26663539139, - "top": 1017.2514257011151 + "top": 522.7829391423746 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -3402,15 +2431,15 @@ "uuid": "9436d70d-95ee-46a6-86c3-60294c3a6967", "when": null, "workflow_outputs": [ - { - "label": "Differential Expression Analysis using DESeq2", - "output_name": "deseq_out", - "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" - }, { "label": "DESeq2 Plots", "output_name": "plots", "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" + }, + { + "label": "Differential Expression Analysis using DESeq2", + "output_name": "deseq_out", + "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" } ] } @@ -3418,6 +2447,6 @@ "tags": [ "RNAseq" ], - "uuid": "9d7f7cff-dbd4-4f0b-a87f-8ab256cd0776", - "version": 9 + "uuid": "2d261afb-e479-4058-a0ec-b606ba65504e", + "version": 1 } \ No newline at end of file From 07710118c6b52c47d788b25b8350ae793a3832eb Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 21 Oct 2024 21:57:59 +0200 Subject: [PATCH 27/47] debug: remove featurecounts and multiqc --- .../rnaseq-pe/rnaseq-pe-tests.yml | 63 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1781 +---------------- 2 files changed, 70 insertions(+), 1774 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index b5cbbfa4a..4233c5e82 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -4,10 +4,6 @@ class: File location: https://zenodo.org/record/4541751/files/Drosophila_melanogaster.BDGP6.87.gtf filetype: gtf - Sample table: - class: File - location: https://zenodo.org/records/13951092/files/Sample_table.tabular - filetype: tabular Collection paired FASTQ files: class: Collection collection_type: list:paired @@ -52,33 +48,12 @@ - class: File identifier: reverse location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger - Generate QC reports?: true Reference genome: dm6 - Use featureCounts for generating count tables: true strandedness: unstranded Compute Cufflinks FPKM?: true GTF with regions to exclude from FPKM normalization with Cufflinks: null Compute StringTie FPKM?: true - DEseq2 batch factors: null outputs: - DESeq2 Plots: - has_size: - size: 33420 - delta: 1500 - Differential Expression Analysis using DESeq2: - asserts: - has_text_matching: - expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" - expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" - MultiQC stats: - asserts: - has_text_matching: - expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*" - expression: "GSM461177_forward\t\t\t\t\t\t\t\t\t\t\t27.95[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" - expression: "GSM461177_reverse\t\t\t\t\t\t\t\t\t\t\t28.22[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" - expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" - expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" - expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" Mapped Reads: element_tests: GSM461177: @@ -150,40 +125,4 @@ GSM461181: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" - Tagged Count Tables: - element_tests: - GSM461177: - asserts: - has_line: - line: "FBgn0017545 6109" - GSM461178: - asserts: - has_line: - line: "FBgn0017545 5649" - GSM461180: - asserts: - has_line: - line: "FBgn0017545 5600" - GSM461181: - asserts: - has_line: - line: "FBgn0017545 5943" - FeatureCounts Summary Table: - element_tests: - GSM461177: - asserts: - has_line: - line: "Assigned 45715" - GSM461178: - asserts: - has_line: - line: "Assigned 38738" - GSM461180: - asserts: - has_line: - line: "Assigned 39998" - GSM461181: - asserts: - has_line: - line: "Assigned 44734" + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 608fd6de1..fe175d630 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -4,43 +4,42 @@ "comments": [ { "child_steps": [ - 13, - 19, - 20 + 9, + 10 ], - "color": "yellow", + "color": "lime", "data": { - "title": "Additional quantification" + "title": "Map Strandedness parameter" }, - "id": 1, + "id": 0, "position": [ - 1306.2, - 919.3315134412595 + 770.5, + 1098.1315134412594 ], "size": [ - 860, - 716 + 251, + 558 ], "type": "frame" }, { "child_steps": [ - 14, - 15, - 16 + 8, + 12, + 13 ], - "color": "lime", + "color": "yellow", "data": { - "title": "Map Strandedness parameter" + "title": "Additional quantification" }, - "id": 0, + "id": 1, "position": [ - 770.5, - 1098.1315134412594 + 1306.2, + 919.3315134412595 ], "size": [ - 251, - 558 + 860, + 716 ], "type": "frame" } @@ -93,43 +92,10 @@ "workflow_outputs": [] }, "1": { - "annotation": "Whether to report QC", - "content_id": null, - "errors": null, - "id": 1, - "input_connections": {}, - "inputs": [ - { - "description": "Whether to report QC", - "name": "Generate QC reports?" - } - ], - "label": "Generate QC reports?", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 40.67737161137343, - "top": 623.2246152658398 - }, - "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "bea331ce-d6fa-4312-8dce-a8b13bc4e77b", - "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "c1ce73d9-f523-4d63-a52a-039977774544" - } - ] - }, - "2": { "annotation": "Select the reference genome", "content_id": null, "errors": null, - "id": 2, + "id": 1, "input_connections": {}, "inputs": [ { @@ -150,19 +116,13 @@ "type": "parameter_input", "uuid": "a72b29ae-65a7-4e4d-a996-2943ab5b02aa", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "52c139e7-d360-4a4e-b6c7-0c5109d791d8" - } - ] + "workflow_outputs": [] }, - "3": { + "2": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, - "id": 3, + "id": 2, "input_connections": {}, "inputs": [ { @@ -185,44 +145,11 @@ "when": null, "workflow_outputs": [] }, - "4": { - "annotation": "Use featureCounts tool instead of RNA STAR?", - "content_id": null, - "errors": null, - "id": 4, - "input_connections": {}, - "inputs": [ - { - "description": "Use featureCounts tool instead of RNA STAR?", - "name": "Use featureCounts for generating count tables" - } - ], - "label": "Use featureCounts for generating count tables", - "name": "Input parameter", - "outputs": [], - "position": { - "left": 160.33752190255188, - "top": 940.765551741371 - }, - "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", - "tool_version": null, - "type": "parameter_input", - "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", - "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "455c5109-a8f2-4fb0-baa9-2863ace00a98" - } - ] - }, - "5": { + "3": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, - "id": 5, + "id": 3, "input_connections": {}, "inputs": [ { @@ -243,19 +170,13 @@ "type": "parameter_input", "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "5b9b3b69-3ffd-47ce-86ed-1ed8ec45f1f1" - } - ] + "workflow_outputs": [] }, - "6": { + "4": { "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, - "id": 6, + "id": 4, "input_connections": {}, "inputs": [ { @@ -276,19 +197,13 @@ "type": "parameter_input", "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a4ca0658-c388-4006-af74-0f0d31b48360" - } - ] + "workflow_outputs": [] }, - "7": { + "5": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 7, + "id": 5, "input_connections": {}, "inputs": [ { @@ -309,19 +224,13 @@ "type": "data_input", "uuid": "0d4e1623-adc9-4ff3-8156-7e1322b1e278", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "892a5cac-97a8-4194-9887-463c741590d9" - } - ] + "workflow_outputs": [] }, - "8": { + "6": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 8, + "id": 6, "input_connections": {}, "inputs": [ { @@ -342,79 +251,13 @@ "type": "parameter_input", "uuid": "056f11f4-bdd9-4361-b037-2c0822320cc2", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "0eb6e8d3-dbb3-486e-b6c2-f7ed2700b5f4" - } - ] - }, - "9": { - "annotation": "Provide experimental and batch details. 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"tool_version": "2.11.40.7+galaxy2", - "type": "tool", - "uuid": "9436d70d-95ee-46a6-86c3-60294c3a6967", - "when": null, - "workflow_outputs": [ - { - "label": "DESeq2 Plots", - "output_name": "plots", - "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" - }, - { - "label": "Differential Expression Analysis using DESeq2", - "output_name": "deseq_out", - "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" + "label": "Genes Expression from Cufflinks", + "output_name": "genes_expression", + "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" } ] } @@ -2447,6 +804,6 @@ "tags": [ "RNAseq" ], - "uuid": "2d261afb-e479-4058-a0ec-b606ba65504e", + "uuid": "64112a66-df88-495c-a4d6-d8487f3704b1", "version": 1 } \ No newline at end of file From 8053bc6e2b4530d5dd3b4dfe13238bbee1b84625 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 21 Oct 2024 22:35:43 +0200 Subject: [PATCH 28/47] debug: only cutadapt and mapping --- .../rnaseq-pe/rnaseq-pe-tests.yml | 60 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 523 +----------------- 2 files changed, 9 insertions(+), 574 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 4233c5e82..db32379c7 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -49,10 +49,6 @@ identifier: reverse location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger Reference genome: dm6 - strandedness: unstranded - Compute Cufflinks FPKM?: true - GTF with regions to exclude from FPKM normalization with Cufflinks: null - Compute StringTie FPKM?: true outputs: Mapped Reads: element_tests: @@ -71,58 +67,4 @@ GSM461181: has_size: value: 3075214 - delta: 150000 - Genes Expression from Cufflinks: - element_tests: - GSM461177: - asserts: - has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" - GSM461178: - asserts: - has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 141422 134823 148020 OK" - GSM461180: - asserts: - has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 134779 128494 141063 OK" - GSM461181: - asserts: - has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 127880 121988 133772 OK" - Transcripts Expression from Cufflinks: - element_tests: - GSM461177: - asserts: - has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" - GSM461178: - asserts: - has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 370.382 128757 122145 135370 OK" - GSM461180: - asserts: - has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 366.172 122426 116120 128732 OK" - GSM461181: - asserts: - has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" - Gene Abundance Estimates from StringTie: - element_tests: - GSM461177: - asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" - GSM461178: - asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t286.68[0-9]*\t143296.84[0-9]*\t365993.15[0-9]*" - GSM461180: - asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t282.60[0-9]*\t138208.90[0-9]*\t367356.56[0-9]*" - GSM461181: - asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" \ No newline at end of file + delta: 150000 \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index fe175d630..dca692f89 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,49 +1,7 @@ { "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", - "comments": [ - { - "child_steps": [ - 9, - 10 - ], - "color": "lime", - "data": { - "title": "Map Strandedness parameter" - }, - "id": 0, - "position": [ - 770.5, - 1098.1315134412594 - ], - "size": [ - 251, - 558 - ], - "type": "frame" - }, - { - "child_steps": [ - 8, - 12, - 13 - ], - "color": "yellow", - "data": { - "title": "Additional quantification" - }, - "id": 1, - "position": [ - 1306.2, - 919.3315134412595 - ], - "size": [ - 860, - 716 - ], - "type": "frame" - } - ], + "comments": [], "creator": [ { "class": "Person", @@ -59,7 +17,7 @@ "format-version": "0.1", "license": "MIT", "release": "0.10", - "name": "rnaseq-pe", + "name": "RNAseq_PE only mapping ", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -146,118 +104,10 @@ "workflow_outputs": [] }, "3": { - 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"tool_version": "2.2.1.3", - "type": "tool", - "uuid": "af5419b7-ae6b-498c-8123-f609b8fcd8b4", - "when": "$(inputs.when)", - "workflow_outputs": [ - { - "label": "Transcripts Expression from Cufflinks", - "output_name": "transcripts_expression", - "uuid": "2c13ef79-948c-4f5f-8516-a769550128fd" - }, - { - "label": "Genes Expression from Cufflinks", - "output_name": "genes_expression", - "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" - } - ] } }, "tags": [ "RNAseq" ], - "uuid": "64112a66-df88-495c-a4d6-d8487f3704b1", - "version": 1 + "uuid": "3d26512e-2045-43f2-a11f-0615e865d507", + "version": 2 } \ No newline at end of file From fadf2ebc6c753f7727589e575ae99d221299887a Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 23 Oct 2024 11:03:14 +0200 Subject: [PATCH 29/47] using chr4-only gtf --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index db32379c7..5a34dec9f 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -2,7 +2,7 @@ job: GTF file of annotation: class: File - location: https://zenodo.org/record/4541751/files/Drosophila_melanogaster.BDGP6.87.gtf + location: https://zenodo.org/records/13951092/files/chr4.gtf filetype: gtf Collection paired FASTQ files: class: Collection From 21768ff7b11133d88a55d206a24646cebb0648db Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 23 Oct 2024 11:21:57 +0200 Subject: [PATCH 30/47] re-add remaning steps --- .../rnaseq-pe/rnaseq-pe-tests.yml | 177 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 3183 ++++++++++++++++- 2 files changed, 3328 insertions(+), 32 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 5a34dec9f..7186101ed 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -4,6 +4,10 @@ class: File location: https://zenodo.org/records/13951092/files/chr4.gtf filetype: gtf + Sample table: + class: File + location: https://zenodo.org/records/13951092/files/Sample_table.tabular + filetype: tabular Collection paired FASTQ files: class: Collection collection_type: list:paired @@ -48,8 +52,34 @@ - class: File identifier: reverse location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger + Generate QC reports?: true Reference genome: dm6 + Use featureCounts for generating count tables: true + strandedness: unstranded + Compute Cufflinks FPKM?: true + GTF with regions to exclude from FPKM normalization with Cufflinks: null + Compute StringTie FPKM?: true + DEseq2 batch factors: null outputs: + DESeq2 Plots: + has_size: + size: 33420 + delta: 1500 + Differential Expression Analysis using DESeq2: + asserts: + has_text_matching: + expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" + expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" + MultiQC stats: + asserts: + has_text_matching: + expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*" + expression: "GSM461177_forward\t\t\t\t\t\t\t\t\t\t\t27.95[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" + expression: "GSM461177_reverse\t\t\t\t\t\t\t\t\t\t\t28.22[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" + expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" + expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + Mapped Reads: element_tests: GSM461177: @@ -67,4 +97,149 @@ GSM461181: has_size: value: 3075214 - delta: 150000 \ No newline at end of file + delta: 150000 + + Genes Expression from Cufflinks: + element_tests: + GSM461177: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + GSM461178: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 141422 134823 148020 OK" + GSM461180: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 134779 128494 141063 OK" + GSM461181: + asserts: + has_line: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 127880 121988 133772 OK" + Transcripts Expression from Cufflinks: + element_tests: + GSM461177: + asserts: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + GSM461178: + asserts: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 370.382 128757 122145 135370 OK" + GSM461180: + asserts: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 366.172 122426 116120 128732 OK" + GSM461181: + asserts: + has_line: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" + Stranded Coverage: + element_tests: + GSM461177_forward: + has_size: + value: 313382 + delta: 15000 + GSM461178_forward: + has_size: + value: 285608 + delta: 15000 + GSM461180_forward: + has_size: + value: 295650 + delta: 15000 + GSM461181_forward: + has_size: + value: 311698 + delta: 15000 + GSM461177_reverse: + has_size: + value: 313241 + delta: 15000 + GSM461178_reverse: + has_size: + value: 281153 + delta: 15000 + GSM461180_reverse: + has_size: + value: 292239 + delta: 15000 + GSM461181_reverse: + has_size: + value: 322248 + delta: 15000 + Unstranded Coverage: + element_tests: + GSM461177: + has_size: + value: 445281 + delta: 20000 + GSM461178: + has_size: + value: 406443 + delta: 20000 + GSM461180: + has_size: + value: 423518 + delta: 20000 + GSM461181: + has_size: + value: 455334 + delta: 20000 + Gene Abundance Estimates from StringTie: + element_tests: + GSM461177: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + GSM461178: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t286.68[0-9]*\t143296.84[0-9]*\t365993.15[0-9]*" + GSM461180: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t282.60[0-9]*\t138208.90[0-9]*\t367356.56[0-9]*" + GSM461181: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" + + Tagged Count Tables: + element_tests: + GSM461177: + asserts: + has_line: + line: "FBgn0017545 6109" + GSM461178: + asserts: + has_line: + line: "FBgn0017545 5649" + GSM461180: + asserts: + has_line: + line: "FBgn0017545 5600" + GSM461181: + asserts: + has_line: + line: "FBgn0017545 5943" + + FeatureCounts Summary Table: + element_tests: + GSM461177: + asserts: + has_line: + line: "Assigned 45715" + GSM461178: + asserts: + has_line: + line: "Assigned 38738" + GSM461180: + asserts: + has_line: + line: "Assigned 39998" + GSM461181: + asserts: + has_line: + line: "Assigned 44734" diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index dca692f89..7101f0647 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,7 +1,70 @@ { "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", - "comments": [], + "comments": [ + { + "child_steps": [ + 21, + 22 + ], + "color": "red", + "data": { + "title": "Coverage Files" + }, + "id": 2, + "position": [ + 2510.1, + 0 + ], + "size": [ + 375, + 538 + ], + "type": "frame" + }, + { + "child_steps": [ + 14, + 15, + 16 + ], + "color": "lime", + "data": { + "title": "Map Strandedness parameter" + }, + "id": 0, + "position": [ + 770.5, + 1592.6 + ], + "size": [ + 251, + 558 + ], + "type": "frame" + }, + { + "child_steps": [ + 13, + 19, + 20 + ], + "color": "yellow", + "data": { + "title": "Additional quantification" + }, + "id": 1, + "position": [ + 1306.2, + 1413.8 + ], + "size": [ + 860, + 716 + ], + "type": "frame" + } + ], "creator": [ { "class": "Person", @@ -17,7 +80,7 @@ "format-version": "0.1", "license": "MIT", "release": "0.10", - "name": "RNAseq_PE only mapping ", + "name": "rnaseq-pe", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -39,7 +102,7 @@ "outputs": [], "position": { "left": 0, - "top": 512.532316262643 + "top": 1007.0008028213834 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -50,11 +113,44 @@ "workflow_outputs": [] }, "1": { - "annotation": "Select the reference genome", + "annotation": "Whether to report QC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, + "inputs": [ + { + "description": "Whether to report QC", + "name": "Generate QC reports?" + } + ], + "label": "Generate QC reports?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 40.67737161137343, + "top": 1117.6931018245803 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "bea331ce-d6fa-4312-8dce-a8b13bc4e77b", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "d9ae5b99-709d-4a01-8b07-216de631e3d4" + } + ] + }, + "2": { + "annotation": "Select the reference genome", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, "inputs": [ { "description": "Select the reference genome", @@ -66,7 +162,7 @@ "outputs": [], "position": { "left": 70.67734212335759, - "top": 734.8603184874431 + "top": 1229.3288050461836 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -74,13 +170,19 @@ "type": "parameter_input", "uuid": "a72b29ae-65a7-4e4d-a996-2943ab5b02aa", "when": null, - "workflow_outputs": [] + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "29c5e09e-8144-45dc-aa55-8c767349c508" + } + ] }, - "2": { + "3": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, - "id": 2, + "id": 3, "input_connections": {}, "inputs": [ { @@ -93,7 +195,7 @@ "outputs": [], "position": { "left": 120.67736637119827, - "top": 832.0321502174164 + "top": 1326.5006367761569 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -103,11 +205,236 @@ "when": null, "workflow_outputs": [] }, - "3": { + "4": { + "annotation": "Use featureCounts tool instead of RNA STAR?", + "content_id": null, + "errors": null, + "id": 4, + "input_connections": {}, + "inputs": [ + { + "description": "Use featureCounts tool instead of RNA STAR?", + "name": "Use featureCounts for generating count tables" + } + ], + "label": "Use featureCounts for generating count tables", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 160.33752190255188, + "top": 1435.2340383001115 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "e65f5234-ab27-4b06-a4c4-5178cf3f32f0" + } + ] + }, + "5": { + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "name": "strandedness" + } + ], + "label": "strandedness", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 203.8828886044653, + "top": 1570.8860110851008 + }, + "tool_id": null, + "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "24881e16-6148-442f-ace3-bc99670d6e21" + } + ] + }, + "6": { + "annotation": "Whether FPKM values should be computed with Cufflinks", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "Whether FPKM values should be computed with Cufflinks", + "name": "Compute Cufflinks FPKM?" + } + ], + "label": "Compute Cufflinks FPKM?", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 228.7717684962176, + "top": 1666.0254709507822 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "a6d6516a-3881-4b6f-b94d-ed5709c53fe3" + } + ] + }, + "7": { + "annotation": "Provide experimental and batch details. 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- "uuid": "3d26512e-2045-43f2-a11f-0615e865d507", - "version": 2 + "uuid": "9d7f7cff-dbd4-4f0b-a87f-8ab256cd0776", + "version": 9 } \ No newline at end of file From bdd0bf90d05cc982a85d760b8967c2f871ab0904 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 23 Oct 2024 14:09:32 +0200 Subject: [PATCH 31/47] re-remove coverage workflows --- .../rnaseq-pe/rnaseq-pe-tests.yml | 56 - .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1495 +++-------------- 2 files changed, 262 insertions(+), 1289 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 7186101ed..900a97de1 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -79,7 +79,6 @@ expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" - Mapped Reads: element_tests: GSM461177: @@ -98,7 +97,6 @@ has_size: value: 3075214 delta: 150000 - Genes Expression from Cufflinks: element_tests: GSM461177: @@ -135,58 +133,6 @@ asserts: has_line: line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" - Stranded Coverage: - element_tests: - GSM461177_forward: - has_size: - value: 313382 - delta: 15000 - GSM461178_forward: - has_size: - value: 285608 - delta: 15000 - GSM461180_forward: - has_size: - value: 295650 - delta: 15000 - GSM461181_forward: - has_size: - value: 311698 - delta: 15000 - GSM461177_reverse: - has_size: - value: 313241 - delta: 15000 - GSM461178_reverse: - has_size: - value: 281153 - delta: 15000 - GSM461180_reverse: - has_size: - value: 292239 - delta: 15000 - GSM461181_reverse: - has_size: - value: 322248 - delta: 15000 - Unstranded Coverage: - element_tests: - GSM461177: - has_size: - value: 445281 - delta: 20000 - GSM461178: - has_size: - value: 406443 - delta: 20000 - GSM461180: - has_size: - value: 423518 - delta: 20000 - GSM461181: - has_size: - value: 455334 - delta: 20000 Gene Abundance Estimates from StringTie: element_tests: GSM461177: @@ -205,7 +151,6 @@ asserts: has_text_matching: expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" - Tagged Count Tables: element_tests: GSM461177: @@ -224,7 +169,6 @@ asserts: has_line: line: "FBgn0017545 5943" - FeatureCounts Summary Table: element_tests: GSM461177: diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 7101f0647..608fd6de1 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -4,21 +4,22 @@ "comments": [ { "child_steps": [ - 21, - 22 + 13, + 19, + 20 ], - "color": "red", + "color": "yellow", "data": { - "title": "Coverage Files" + "title": "Additional quantification" }, - "id": 2, + "id": 1, "position": [ - 2510.1, - 0 + 1306.2, + 919.3315134412595 ], "size": [ - 375, - 538 + 860, + 716 ], "type": "frame" }, @@ -35,34 +36,13 @@ "id": 0, "position": [ 770.5, - 1592.6 + 1098.1315134412594 ], "size": [ 251, 558 ], "type": "frame" - }, - { - "child_steps": [ - 13, - 19, - 20 - ], - "color": "yellow", - "data": { - "title": "Additional quantification" - }, - "id": 1, - "position": [ - 1306.2, - 1413.8 - ], - "size": [ - 860, - 716 - ], - "type": "frame" } ], "creator": [ @@ -102,7 +82,7 @@ "outputs": [], "position": { "left": 0, - "top": 1007.0008028213834 + "top": 512.532316262643 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -129,7 +109,7 @@ "outputs": [], "position": { "left": 40.67737161137343, - "top": 1117.6931018245803 + "top": 623.2246152658398 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -141,7 +121,7 @@ { "label": null, "output_name": "output", - "uuid": "d9ae5b99-709d-4a01-8b07-216de631e3d4" + "uuid": "c1ce73d9-f523-4d63-a52a-039977774544" } ] }, @@ -162,7 +142,7 @@ "outputs": [], "position": { "left": 70.67734212335759, - "top": 1229.3288050461836 + "top": 734.8603184874431 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -174,7 +154,7 @@ { "label": null, "output_name": "output", - "uuid": "29c5e09e-8144-45dc-aa55-8c767349c508" + "uuid": "52c139e7-d360-4a4e-b6c7-0c5109d791d8" } ] }, @@ -195,7 +175,7 @@ "outputs": [], "position": { "left": 120.67736637119827, - "top": 1326.5006367761569 + "top": 832.0321502174164 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -222,7 +202,7 @@ "outputs": [], "position": { "left": 160.33752190255188, - "top": 1435.2340383001115 + "top": 940.765551741371 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -234,7 +214,7 @@ { "label": null, "output_name": "output", - "uuid": "e65f5234-ab27-4b06-a4c4-5178cf3f32f0" + "uuid": "455c5109-a8f2-4fb0-baa9-2863ace00a98" } ] }, @@ -255,7 +235,7 @@ "outputs": [], "position": { "left": 203.8828886044653, - "top": 1570.8860110851008 + "top": 1076.4175245263605 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -267,7 +247,7 @@ { "label": null, "output_name": "output", - "uuid": "24881e16-6148-442f-ace3-bc99670d6e21" + "uuid": "5b9b3b69-3ffd-47ce-86ed-1ed8ec45f1f1" } ] }, @@ -288,7 +268,7 @@ "outputs": [], "position": { "left": 228.7717684962176, - "top": 1666.0254709507822 + "top": 1171.5569843920416 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -300,42 +280,15 @@ { "label": null, "output_name": "output", - "uuid": "a6d6516a-3881-4b6f-b94d-ed5709c53fe3" + "uuid": "a4ca0658-c388-4006-af74-0f0d31b48360" } ] }, "7": { - "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "content_id": null, - "errors": null, - "id": 7, - "input_connections": {}, - "inputs": [ - { - "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "name": "Sample table" - } - ], - "label": "Sample table", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1462.1645523806205, - "top": 909.2581294996864 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", - "when": null, - "workflow_outputs": [] - }, - "8": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 8, + "id": 7, "input_connections": {}, "inputs": [ { @@ -348,7 +301,7 @@ "outputs": [], "position": { "left": 260.1137371795465, - "top": 1784.313630812311 + "top": 1289.8451442535707 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -360,15 +313,15 @@ { "label": null, "output_name": "output", - "uuid": "c4058f91-dda0-4063-beaa-33505d1754d1" + "uuid": "892a5cac-97a8-4194-9887-463c741590d9" } ] }, - "9": { + "8": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 9, + "id": 8, "input_connections": {}, "inputs": [ { @@ -381,7 +334,7 @@ "outputs": [], "position": { "left": 268.7808865853354, - "top": 1905.5010561327158 + "top": 1411.0325695739753 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -393,10 +346,37 @@ { "label": null, "output_name": "output", - "uuid": "51b56f88-8607-4fc5-b958-19bd1ca31901" + "uuid": "0eb6e8d3-dbb3-486e-b6c2-f7ed2700b5f4" } ] }, + "9": { + "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "content_id": null, + "errors": null, + "id": 9, + "input_connections": {}, + "inputs": [ + { + "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "name": "Sample table" + } + ], + "label": "Sample table", + "name": "Input dataset", + "outputs": [], + "position": { + "left": 1462.1645523806205, + "top": 414.789642940946 + }, + "tool_id": null, + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", + "tool_version": null, + "type": "data_input", + "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", + "when": null, + "workflow_outputs": [] + }, "10": { "annotation": "Tabular file with additional batch factors to include in the model", "content_id": null, @@ -414,7 +394,7 @@ "outputs": [], "position": { "left": 2203.102316887585, - "top": 1355.0225413410844 + "top": 860.554054782344 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": null}", @@ -426,7 +406,7 @@ { "label": null, "output_name": "output", - "uuid": "c1ac1a43-8bb1-44d4-8f88-540cb2ab7852" + "uuid": "ae3cb027-73f5-41b9-a2e7-2a2fdabd37b7" } ] }, @@ -461,7 +441,7 @@ ], "position": { "left": 239.35765144976227, - 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"top": 16.0 + "top": 16 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1", @@ -2329,7 +1358,7 @@ ], "position": { "left": 282.1421365930926, - "top": 0.0 + "top": 0 }, "post_job_actions": { "ChangeDatatypeActionoutput": { @@ -2469,7 +1498,7 @@ ], "position": { "left": 842.1422267022583, - "top": 16.0 + "top": 16 }, "post_job_actions": { "RenameDatasetActiondata_param": { @@ -2657,7 +1686,7 @@ { "label": null, "output_name": "3:output", - "uuid": "f8d298cc-b2c6-43d7-8904-32f1ec1e7c50" + "uuid": "17690e9c-c087-41b6-a4d2-ec77d82f285f" }, { "label": "FeatureCounts Summary Table", @@ -2671,9 +1700,9 @@ } ] }, - "24": { + "22": { "annotation": "", - "id": 24, + "id": 22, "input_connections": { "Cutadapt Reports": { "id": 11, @@ -2696,7 +1725,7 @@ "output_name": "mapped_reads" }, "featureCounts summaries": { - "id": 23, + "id": 21, "input_subworkflow_step_id": 1, "output_name": "FeatureCounts Summary Table" }, @@ -2721,7 +1750,7 @@ "outputs": [], "position": { "left": 2581.8385293658202, - "top": 574.7767421741249 + "top": 80.3082556153845 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3332,11 +2361,11 @@ } ] }, - "25": { + "23": { "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "errors": null, - "id": 25, + "id": 23, "input_connections": { "batch_factors": { "id": 10, @@ -3347,7 +2376,7 @@ "output_name": "output" }, "select_data|countsFile": { - "id": 23, + "id": 21, "output_name": "Tagged Count Tables" } }, @@ -3371,7 +2400,7 @@ ], "position": { "left": 2566.26663539139, - "top": 1017.2514257011151 + "top": 522.7829391423746 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -3402,15 +2431,15 @@ "uuid": "9436d70d-95ee-46a6-86c3-60294c3a6967", "when": null, "workflow_outputs": [ - { - "label": "Differential Expression Analysis using DESeq2", - "output_name": "deseq_out", - "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" - }, { "label": "DESeq2 Plots", "output_name": "plots", "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" + }, + { + "label": "Differential Expression Analysis using DESeq2", + "output_name": "deseq_out", + "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" } ] } @@ -3418,6 +2447,6 @@ "tags": [ "RNAseq" ], - "uuid": "9d7f7cff-dbd4-4f0b-a87f-8ab256cd0776", - "version": 9 + "uuid": "2d261afb-e479-4058-a0ec-b606ba65504e", + "version": 1 } \ No newline at end of file From c0569455045fa579392e74d69074d7b7b3ebf71d Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 23 Oct 2024 14:41:47 +0200 Subject: [PATCH 32/47] do not use featurecounts --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 900a97de1..bae4607b4 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -54,7 +54,7 @@ location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger Generate QC reports?: true Reference genome: dm6 - Use featureCounts for generating count tables: true + Use featureCounts for generating count tables: false strandedness: unstranded Compute Cufflinks FPKM?: true GTF with regions to exclude from FPKM normalization with Cufflinks: null From a424cd823f1b05e096c079b5aed1c4be2f33831b Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 23 Oct 2024 15:32:43 +0200 Subject: [PATCH 33/47] remove featurecounts step --- .../transcriptomics/rnaseq-pe/CHANGELOG.md | 2 +- .../rnaseq-pe/rnaseq-pe-tests.yml | 19 - .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 2212 ++++++++++++----- 3 files changed, 1526 insertions(+), 707 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 1f1bec2eb..0345757ab 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -3,7 +3,7 @@ ## [0.10] 2024-09-23 ### Manual update -- Using a new subsampled test data from Zenodo record https://zenodo.org/records/13888221 +- Using a new subsampled test data from Zenodo record https://zenodo.org/records/13951092 - Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, Picard reports - Added DESeq2 step that uses tags to choose factors diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index bae4607b4..fbbaef0e1 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -54,7 +54,6 @@ location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger Generate QC reports?: true Reference genome: dm6 - Use featureCounts for generating count tables: false strandedness: unstranded Compute Cufflinks FPKM?: true GTF with regions to exclude from FPKM normalization with Cufflinks: null @@ -169,21 +168,3 @@ asserts: has_line: line: "FBgn0017545 5943" - FeatureCounts Summary Table: - element_tests: - GSM461177: - asserts: - has_line: - line: "Assigned 45715" - GSM461178: - asserts: - has_line: - line: "Assigned 38738" - GSM461180: - asserts: - has_line: - line: "Assigned 39998" - GSM461181: - asserts: - has_line: - line: "Assigned 44734" diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 608fd6de1..a3c494526 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,33 +1,31 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", + "annotation": "without featurecounts", "comments": [ { "child_steps": [ - 13, 19, 20 ], - "color": "yellow", + "color": "red", "data": { - "title": "Additional quantification" + "title": "Coverage Files" }, - "id": 1, + "id": 2, "position": [ - 1306.2, - 919.3315134412595 + 2510.1, + 0 ], "size": [ - 860, - 716 + 375, + 538 ], "type": "frame" }, { "child_steps": [ - 14, - 15, - 16 + 13, + 14 ], "color": "lime", "data": { @@ -36,13 +34,34 @@ "id": 0, "position": [ 770.5, - 1098.1315134412594 + 1592.6 ], "size": [ 251, 558 ], "type": "frame" + }, + { + "child_steps": [ + 12, + 17, + 18 + ], + "color": "yellow", + "data": { + "title": "Additional quantification" + }, + "id": 1, + "position": [ + 1306.2, + 1413.8 + ], + "size": [ + 860, + 716 + ], + "type": "frame" } ], "creator": [ @@ -59,8 +78,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.10", - "name": "rnaseq-pe", + "name": "rnaseq-pe-wo-featurecunts", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -82,7 +100,7 @@ "outputs": [], "position": { "left": 0, - "top": 512.532316262643 + "top": 1007.0008028213834 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -109,7 +127,7 @@ "outputs": [], "position": { "left": 40.67737161137343, - "top": 623.2246152658398 + "top": 1117.6931018245803 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -121,7 +139,7 @@ { "label": null, "output_name": "output", - "uuid": "c1ce73d9-f523-4d63-a52a-039977774544" + "uuid": "40d42867-028e-4a4c-85f4-ef0f28e5114e" } ] }, @@ -142,7 +160,7 @@ "outputs": [], "position": { "left": 70.67734212335759, - "top": 734.8603184874431 + "top": 1229.3288050461836 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -154,7 +172,7 @@ { "label": null, "output_name": "output", - "uuid": "52c139e7-d360-4a4e-b6c7-0c5109d791d8" + "uuid": "6413a62e-311d-4c7d-8d94-7a43c2cbe5b1" } ] }, @@ -175,7 +193,7 @@ "outputs": [], "position": { "left": 120.67736637119827, - "top": 832.0321502174164 + "top": 1326.5006367761569 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -186,103 +204,97 @@ "workflow_outputs": [] }, "4": { - "annotation": "Use featureCounts tool instead of RNA STAR?", + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, "id": 4, "input_connections": {}, "inputs": [ { - "description": "Use featureCounts tool instead of RNA STAR?", - "name": "Use featureCounts for generating count tables" + "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "name": "strandedness" } ], - "label": "Use featureCounts for generating count tables", + "label": "strandedness", "name": "Input parameter", "outputs": [], "position": { - "left": 160.33752190255188, - 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"description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", - "name": "strandedness" + "description": "Whether FPKM values should be computed with Cufflinks", + "name": "Compute Cufflinks FPKM?" } ], - "label": "strandedness", + "label": "Compute Cufflinks FPKM?", "name": "Input parameter", "outputs": [], "position": { - "left": 203.8828886044653, - "top": 1076.4175245263605 + "left": 228.7717684962176, + "top": 1666.0254709507822 }, "tool_id": null, - "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", + "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", "when": null, "workflow_outputs": [ { "label": null, "output_name": "output", - "uuid": "5b9b3b69-3ffd-47ce-86ed-1ed8ec45f1f1" + "uuid": "ccbcf8d7-cee8-4cb9-b96f-d320b392a0dd" } ] }, "6": { - "annotation": "Whether FPKM values should be computed with Cufflinks", + "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "Whether FPKM values should be computed with Cufflinks", - "name": "Compute Cufflinks FPKM?" + "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", + "name": "Sample table" } ], - "label": "Compute Cufflinks FPKM?", - "name": "Input parameter", + "label": "Sample table", + "name": "Input dataset", "outputs": [], "position": { - "left": 228.7717684962176, - "top": 1171.5569843920416 + "left": 1462.1645523806205, + "top": 909.2581294996864 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", "tool_version": null, - "type": "parameter_input", - "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", + "type": "data_input", + "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a4ca0658-c388-4006-af74-0f0d31b48360" - } - ] + "workflow_outputs": [] }, "7": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -301,7 +313,7 @@ "outputs": [], "position": { "left": 260.1137371795465, - "top": 1289.8451442535707 + "top": 1784.313630812311 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -313,7 +325,7 @@ { "label": null, "output_name": "output", - "uuid": "892a5cac-97a8-4194-9887-463c741590d9" + "uuid": "93540fa2-508e-46f4-b603-b26f9b6d3fef" } ] }, @@ -334,7 +346,7 @@ "outputs": [], "position": { "left": 268.7808865853354, - "top": 1411.0325695739753 + "top": 1905.5010561327158 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -346,42 +358,15 @@ { "label": null, "output_name": "output", - "uuid": "0eb6e8d3-dbb3-486e-b6c2-f7ed2700b5f4" + "uuid": "642c3eee-8c90-4e1e-8962-f922f004acdb" } ] }, "9": { - "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "content_id": null, - "errors": null, - "id": 9, - "input_connections": {}, - "inputs": [ - { - "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "name": "Sample table" - } - ], - "label": "Sample table", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1462.1645523806205, - "top": 414.789642940946 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", - "when": null, - "workflow_outputs": [] - }, - "10": { "annotation": "Tabular file with additional batch factors to include in the model", "content_id": null, "errors": null, - "id": 10, + "id": 9, "input_connections": {}, "inputs": [ { @@ -394,7 +379,7 @@ "outputs": [], "position": { "left": 2203.102316887585, - "top": 860.554054782344 + "top": 1355.0225413410844 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": null}", @@ -406,15 +391,15 @@ { "label": null, "output_name": "output", - "uuid": "ae3cb027-73f5-41b9-a2e7-2a2fdabd37b7" + "uuid": "43042d3f-718d-4c03-9c2f-682cd2b9eab0" } ] }, - 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"Tagged Count Tables", - "uuid": "a4e352a1-ca84-4e0b-91f6-1b1a5381d183" + "label": null, + "output_name": "0:output", + "uuid": "331cab31-e78d-448b-88aa-7368e0ee619b" } ] }, - "22": { + "21": { "annotation": "", - "id": 22, + "id": 21, "input_connections": { "Cutadapt Reports": { - "id": 11, + "id": 10, "input_subworkflow_step_id": 2, "output_name": "report" }, "FASTQ collection": { - "id": 12, + "id": 11, "input_subworkflow_step_id": 0, "output_name": "output" }, "STAR logs": { - "id": 17, + "id": 15, "input_subworkflow_step_id": 3, "output_name": "output_log" }, "STAR paired-end BAM": { - "id": 17, + "id": 15, "input_subworkflow_step_id": 5, "output_name": "mapped_reads" }, "featureCounts summaries": { - "id": 21, + "id": 16, "input_subworkflow_step_id": 1, "output_name": "FeatureCounts Summary Table" }, @@ -1750,7 +2588,7 @@ "outputs": [], "position": { "left": 2581.8385293658202, - "top": 80.3082556153845 + "top": 574.7767421741249 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2361,26 +3199,26 @@ } ] }, - "23": { + "22": { "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "errors": null, - "id": 23, + "id": 22, "input_connections": { "batch_factors": { - "id": 10, - "output_name": "output" - }, - "header": { - "id": 4, + "id": 9, "output_name": "output" }, "select_data|countsFile": { - "id": 21, + "id": 16, "output_name": "Tagged Count Tables" } }, "inputs": [ + { + "description": "runtime parameter for tool DESeq2", + "name": "batch_factors" + }, { "description": "runtime parameter for tool DESeq2", "name": "select_data" @@ -2400,7 +3238,7 @@ ], "position": { "left": 2566.26663539139, - "top": 522.7829391423746 + "top": 1017.2514257011151 }, "post_job_actions": { "RenameDatasetActiondeseq_out": { @@ -2425,21 +3263,21 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"ConnectedValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"header\": false, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.11.40.7+galaxy2", "type": "tool", "uuid": "9436d70d-95ee-46a6-86c3-60294c3a6967", "when": null, "workflow_outputs": [ - { - "label": "DESeq2 Plots", - "output_name": "plots", - "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" - }, { "label": "Differential Expression Analysis using DESeq2", "output_name": "deseq_out", "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" + }, + { + "label": "DESeq2 Plots", + "output_name": "plots", + "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" } ] } @@ -2447,6 +3285,6 @@ "tags": [ "RNAseq" ], - "uuid": "2d261afb-e479-4058-a0ec-b606ba65504e", + "uuid": "c85f7231-8058-4809-b83b-bc4d079c3b61", "version": 1 } \ No newline at end of file From 7c89957a9e7bedeb7e0638ebca709c93e69eb827 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 24 Oct 2024 17:16:04 +0200 Subject: [PATCH 34/47] Use a new test dataset from Yeast --- .../rnaseq-pe/rnaseq-pe-tests.yml | 214 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 2780 +++++++++-------- .../rnaseq-pe/test-data/Sample table.tabular | 4 - 3 files changed, 1624 insertions(+), 1374 deletions(-) delete mode 100644 workflows/transcriptomics/rnaseq-pe/test-data/Sample table.tabular diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index fbbaef0e1..395a5d20b 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -2,11 +2,11 @@ job: GTF file of annotation: class: File - location: https://zenodo.org/records/13951092/files/chr4.gtf + location: https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf filetype: gtf Sample table: class: File - location: https://zenodo.org/records/13951092/files/Sample_table.tabular + location: https://zenodo.org/records/13987631/files/sample_table.tabular filetype: tabular Collection paired FASTQ files: class: Collection @@ -14,61 +14,54 @@ elements: - class: Collection type: paired - identifier: GSM461177 + identifier: SRR5085167 elements: - class: File identifier: forward - location: https://zenodo.org/records/13951092/files/GSM461177_1.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085167_forward.fastqsanger.gz - class: File identifier: reverse - location: https://zenodo.org/records/13951092/files/GSM461177_2.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085167_reverse.fastqsanger.gz - class: Collection type: paired - identifier: GSM461178 + identifier: SRR5085168 elements: - class: File identifier: forward - location: https://zenodo.org/records/13951092/files/GSM461178_1.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085168_forward.fastqsanger.gz - class: File identifier: reverse - location: https://zenodo.org/records/13951092/files/GSM461178_2.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085168_reverse.fastqsanger.gz - class: Collection type: paired - identifier: GSM461180 + identifier: SRR5085169 elements: - class: File identifier: forward - location: https://zenodo.org/records/13951092/files/GSM461180_1.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085169_forward.fastqsanger.gz - class: File identifier: reverse - location: https://zenodo.org/records/13951092/files/GSM461180_2.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085169_reverse.fastqsanger.gz - class: Collection type: paired - identifier: GSM461181 + identifier: SRR5085170 elements: - class: File identifier: forward - location: https://zenodo.org/records/13951092/files/GSM461181_1.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085170_forward.fastqsanger.gz - class: File identifier: reverse - location: https://zenodo.org/records/13951092/files/GSM461181_2.fastqsanger + location: https://zenodo.org/records/13987631/files/SRR5085170_reverse.fastqsanger.gz + Forward adapter: AGATCGGAAGAG + Reverse adapter: GATCGTCGGACT Generate QC reports?: true - Reference genome: dm6 - strandedness: unstranded + Reference genome: sacCer3 + Use featureCounts for generating count tables: true + strandedness: stranded - forward Compute Cufflinks FPKM?: true GTF with regions to exclude from FPKM normalization with Cufflinks: null Compute StringTie FPKM?: true - DEseq2 batch factors: null outputs: - DESeq2 Plots: - has_size: - size: 33420 - delta: 1500 - Differential Expression Analysis using DESeq2: - asserts: - has_text_matching: - expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" - expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" MultiQC stats: asserts: has_text_matching: @@ -78,93 +71,172 @@ expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + DESeq2 Plots: + has_size: + size: 33420 + delta: 1500 + Differential Expression Analysis using DESeq2: + asserts: + has_text_matching: + expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" + expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" + Stranded Coverage: + element_tests: + SRR5085167_forward: + has_size: + value: 3058282 + delta: 150000 + SRR5085168_forward: + has_size: + value: 3058282 + delta: 150000 + SRR5085169_forward: + has_size: + value: 3058282 + delta: 150000 + SRR5085170_forward: + has_size: + value: 3058282 + delta: 150000 + SRR5085167_reverse: + has_size: + value: 3058282 + delta: 150000 + SRR5085168_reverse: + has_size: + value: 3058282 + delta: 150000 + SRR5085169_reverse: + has_size: + value: 3058282 + delta: 150000 + SRR5085170_reverse: + has_size: + value: 3058282 + delta: 150000 + Gene Abundance Estimates from StringTie: + element_tests: + SRR5085167: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + SRR5085168: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + SRR5085169: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + SRR5085170: + asserts: + has_text_matching: + expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + Unstranded Coverage: + element_tests: + SRR5085167: + has_size: + value: 3058282 + delta: 150000 + SRR5085168: + has_size: + value: 3058282 + delta: 150000 + SRR5085169: + has_size: + value: 3058282 + delta: 150000 + SRR5085170: + has_size: + value: 3058282 + delta: 150000 Mapped Reads: element_tests: - GSM461177: + SRR5085167: has_size: value: 3058282 delta: 150000 - GSM461178: + SRR5085168: has_size: - value: 3032322 + value: 3058282 delta: 150000 - GSM461180: + SRR5085169: has_size: - value: 3165439 + value: 3058282 delta: 150000 - GSM461181: + SRR5085170: has_size: - value: 3075214 + value: 3058282 delta: 150000 Genes Expression from Cufflinks: element_tests: - GSM461177: + SRR5085167: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" - GSM461178: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + SRR5085168: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 141422 134823 148020 OK" - GSM461180: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + SRR5085169: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 134779 128494 141063 OK" - GSM461181: + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + SRR5085170: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 127880 121988 133772 OK" + line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" Transcripts Expression from Cufflinks: element_tests: - GSM461177: + SRR5085167: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" - GSM461178: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + SRR5085168: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 370.382 128757 122145 135370 OK" - GSM461180: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + SRR5085169: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 366.172 122426 116120 128732 OK" - GSM461181: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + SRR5085170: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 404.198 115973 110059 121886 OK" - Gene Abundance Estimates from StringTie: + line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + Tagged Count Tables: element_tests: - GSM461177: + SRR5085167: asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" - GSM461178: + has_line: + line: "FBgn0017545 6109" + SRR5085168: asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t286.68[0-9]*\t143296.84[0-9]*\t365993.15[0-9]*" - GSM461180: + has_line: + line: "FBgn0017545 6109" + SRR5085169: asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t282.60[0-9]*\t138208.90[0-9]*\t367356.56[0-9]*" - GSM461181: + has_line: + line: "FBgn0017545 6109" + SRR5085170: asserts: - has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t316.33[0-9]*\t129439.64[0-9]*\t344739.90[0-9]*" - Tagged Count Tables: + has_line: + line: "FBgn0017545 6109" + FeatureCounts Summary Table: element_tests: - GSM461177: + SRR5085167: asserts: has_line: - line: "FBgn0017545 6109" - GSM461178: + line: "Assigned 45715" + SRR5085168: asserts: has_line: - line: "FBgn0017545 5649" - GSM461180: + line: "Assigned 45715" + SRR5085169: asserts: has_line: - line: "FBgn0017545 5600" - GSM461181: + line: "Assigned 45715" + SRR5085170: asserts: has_line: - line: "FBgn0017545 5943" + line: "Assigned 45715" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index a3c494526..073e5ce57 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,11 +1,11 @@ { "a_galaxy_workflow": "true", - "annotation": "without featurecounts", + "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", "comments": [ { "child_steps": [ - 19, - 20 + 22, + 23 ], "color": "red", "data": { @@ -13,7 +13,7 @@ }, "id": 2, "position": [ - 2510.1, + 2586.921132334357, 0 ], "size": [ @@ -24,8 +24,9 @@ }, { "child_steps": [ - 13, - 14 + 15, + 16, + 17 ], "color": "lime", "data": { @@ -33,7 +34,7 @@ }, "id": 0, "position": [ - 770.5, + 847.321132334357, 1592.6 ], "size": [ @@ -44,9 +45,9 @@ }, { "child_steps": [ - 12, - 17, - 18 + 14, + 20, + 21 ], "color": "yellow", "data": { @@ -54,7 +55,7 @@ }, "id": 1, "position": [ - 1306.2, + 1383.0211323343572, 1413.8 ], "size": [ @@ -78,17 +79,84 @@ ], "format-version": "0.1", "license": "MIT", - "name": "rnaseq-pe-wo-featurecunts", + "release": "0.10", + "name": "rnaseq-pe", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, "steps": { "0": { - "annotation": "Should be a list of paired-end RNA-seq fastqs", + "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "content_id": null, "errors": null, "id": 0, "input_connections": {}, + "inputs": [ + { + "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "name": "Forward adapter" + } + ], + "label": "Forward adapter", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 0, + "top": 733.4300127682214 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "6d1de206-97c4-41ba-8702-a980f748a689", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "349d9805-89b8-4b7c-94ec-17f1bc19f2a0" + } + ] + }, + "1": { + "annotation": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "content_id": null, + "errors": null, + "id": 1, + "input_connections": {}, + "inputs": [ + { + "description": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "name": "Reverse adapter" + } + ], + "label": "Reverse adapter", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 43.382193674328164, + "top": 856.5124765005733 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "7aae38b8-39a8-4fba-bc6b-bda8c1ea9162", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "f43a77a2-f04a-4713-b1ab-04e9223ab8fa" + } + ] + }, + "2": { + "annotation": "Should be a list of paired-end RNA-seq fastqs", + "content_id": null, + "errors": null, + "id": 2, + "input_connections": {}, "inputs": [ { "description": "Should be a list of paired-end RNA-seq fastqs", @@ -99,7 +167,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0, + "left": 76.82113233435703, "top": 1007.0008028213834 }, "tool_id": null, @@ -110,11 +178,11 @@ "when": null, "workflow_outputs": [] }, - "1": { + "3": { "annotation": "Whether to report QC", "content_id": null, "errors": null, - "id": 1, + "id": 3, "input_connections": {}, "inputs": [ { @@ -126,7 +194,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 40.67737161137343, + "left": 117.49850394573046, "top": 1117.6931018245803 }, "tool_id": null, @@ -139,15 +207,15 @@ { "label": null, "output_name": "output", - "uuid": "40d42867-028e-4a4c-85f4-ef0f28e5114e" + "uuid": "78e6bb9a-69af-449b-ad5f-7c1c8296bdaf" } ] }, - "2": { + "4": { "annotation": "Select the reference genome", "content_id": null, "errors": null, - "id": 2, + "id": 4, "input_connections": {}, "inputs": [ { @@ -159,7 +227,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 70.67734212335759, + "left": 147.49847445771462, "top": 1229.3288050461836 }, "tool_id": null, @@ -172,15 +240,15 @@ { "label": null, "output_name": "output", - "uuid": "6413a62e-311d-4c7d-8d94-7a43c2cbe5b1" + "uuid": "5778573f-950f-43eb-aa84-8e4191df8b0c" } ] }, - "3": { + "5": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", "content_id": null, "errors": null, - "id": 3, + "id": 5, "input_connections": {}, "inputs": [ { @@ -192,7 +260,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 120.67736637119827, + "left": 197.4984987055553, "top": 1326.5006367761569 }, "tool_id": null, @@ -203,11 +271,44 @@ "when": null, "workflow_outputs": [] }, - "4": { + "6": { + "annotation": "Use featureCounts tool instead of RNA STAR?", + "content_id": null, + "errors": null, + "id": 6, + "input_connections": {}, + "inputs": [ + { + "description": "Use featureCounts tool instead of RNA STAR?", + "name": "Use featureCounts for generating count tables" + } + ], + "label": "Use featureCounts for generating count tables", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 237.15865423690892, + "top": 1435.2340383001115 + }, + "tool_id": null, + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", + "when": null, + "workflow_outputs": [ + { + "label": null, + "output_name": "output", + "uuid": "0d981cb2-b09c-4fbc-a0cc-eded4a12a801" + } + ] + }, + "7": { "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, - "id": 4, + "id": 7, "input_connections": {}, "inputs": [ { @@ -219,7 +320,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 203.8828886044653, + "left": 280.70402093882234, "top": 1570.8860110851008 }, "tool_id": null, @@ -232,15 +333,15 @@ { "label": null, "output_name": "output", - "uuid": "c4ac27c9-c420-4f03-89a8-98beee41f9ca" + "uuid": "1b3d905c-be93-46ad-b58e-cdf5bbdbf6eb" } ] }, - "5": { + "8": { "annotation": "Whether FPKM values should be computed with Cufflinks", "content_id": null, "errors": null, - "id": 5, + "id": 8, "input_connections": {}, "inputs": [ { @@ -252,7 +353,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 228.7717684962176, + "left": 305.59290083057465, "top": 1666.0254709507822 }, "tool_id": null, @@ -265,15 +366,15 @@ { "label": null, "output_name": "output", - "uuid": "ccbcf8d7-cee8-4cb9-b96f-d320b392a0dd" + "uuid": "8e9a31f7-0da5-4aae-8ec8-54bc28fbb979" } ] }, - "6": { + "9": { "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", "content_id": null, "errors": null, - "id": 6, + "id": 9, "input_connections": {}, "inputs": [ { @@ -285,7 +386,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 1462.1645523806205, + "left": 1538.9856847149777, "top": 909.2581294996864 }, "tool_id": null, @@ -296,11 +397,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "10": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 7, + "id": 10, "input_connections": {}, "inputs": [ { @@ -312,7 +413,7 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 260.1137371795465, + "left": 336.93486951390355, "top": 1784.313630812311 }, "tool_id": null, @@ -325,15 +426,15 @@ { "label": null, "output_name": "output", - "uuid": "93540fa2-508e-46f4-b603-b26f9b6d3fef" + "uuid": "5b5095cc-6934-4336-9321-028436a11344" } ] }, - "8": { + "11": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 8, + "id": 11, "input_connections": {}, "inputs": [ { @@ -345,7 +446,7 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 268.7808865853354, + "left": 345.60201891969245, "top": 1905.5010561327158 }, "tool_id": null, @@ -358,52 +459,27 @@ { "label": null, "output_name": "output", - "uuid": "642c3eee-8c90-4e1e-8962-f922f004acdb" - } - ] - }, - "9": { - "annotation": "Tabular file with additional batch factors to include in the model", - "content_id": null, - "errors": null, - "id": 9, - "input_connections": {}, - "inputs": [ - { - "description": "Tabular file with additional batch factors to include in the model", - "name": "DEseq2 batch factors" - } - ], - "label": "DEseq2 batch factors", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 2203.102316887585, - "top": 1355.0225413410844 - }, - "tool_id": null, - "tool_state": "{\"optional\": true, \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "6abd6f58-1f0a-477c-9783-6f8dcfafb77d", - "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "43042d3f-718d-4c03-9c2f-682cd2b9eab0" + "uuid": "5b7df78b-f88d-4ef5-9e70-938adcf11bfa" } ] }, - "10": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 10, + "id": 12, "input_connections": { "library|input_1": { + "id": 2, + "output_name": "output" + }, + "library|r1|adapters_0|adapter_source|adapter": { "id": 0, "output_name": "output" + }, + "library|r2|adapters2_0|adapter_source|adapter": { + "id": 1, + "output_name": "output" } }, "inputs": [ @@ -425,8 +501,8 @@ } ], "position": { - "left": 239.35765144976227, - "top": 494.46848655874044 + "left": 374.33462420145804, + "top": 607.862671571285 }, "post_job_actions": { "HideDatasetActionout1": { @@ -452,21 +528,21 @@ "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [], \"front_adapters\": [], \"anywhere_adapters\": []}, \"r2\": {\"adapters2\": [], \"front_adapters2\": [], \"anywhere_adapters2\": []}, \"pair_adapters\": false}, \"other_trimming_options\": {\"cut\": \"0\", \"cut2\": \"0\", \"quality_cutoff\": \"30\", \"quality_cutoff2\": \"\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"poly_a\": false, \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"shorten_options_r2\": {\"shorten_values_r2\": \"False\", \"__current_case__\": 1}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"strip_suffix\": \"\", \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"adapter_options\": {\"action\": \"trim\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": false, \"no_match_adapter_wildcards\": true, \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"minimum_length2\": null, \"maximum_length\": null, \"maximum_length2\": null, \"max_n\": null, \"max_expected_errors\": null, \"max_average_error_rate\": null, \"discard_casava\": false, \"pair_filter\": \"any\"}, \"library\": {\"type\": \"paired_collection\", \"__current_case__\": 2, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - 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"11": { + "13": { "annotation": "", "content_id": "__FLATTEN__", "errors": null, - "id": 11, + "id": 13, "input_connections": { "input": { - "id": 0, + "id": 2, "output_name": "output" } }, @@ -480,7 +556,7 @@ } ], "position": { - "left": 345.7624932537463, + "left": 422.58362558810336, "top": 963.9873433527641 }, "post_job_actions": {}, @@ -492,14 +568,14 @@ "when": null, "workflow_outputs": [] }, - "12": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 12, + "id": 14, "input_connections": { "components_0|param_type|component_value": { - "id": 2, + "id": 4, "output_name": "output" } }, @@ -513,7 +589,7 @@ } ], "position": { - "left": 1412.7865078407585, + "left": 1489.6076401751156, "top": 1513.204961480357 }, "post_job_actions": { @@ -537,14 +613,64 @@ "when": null, "workflow_outputs": [] }, - "13": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 13, + "id": 15, "input_connections": { "input_param_type|input_param": { - "id": 4, + "id": 7, + "output_name": "output" + } + }, + "inputs": [ + { + "description": "runtime parameter for tool Map parameter value", + "name": "input_param_type" + } + ], + "label": "Get featureCounts strandedness parameter", + "name": "Map parameter value", + "outputs": [ + { + "name": "output_param_text", + "type": "expression.json" + } + ], + "position": { + "left": 871.929384855411, + "top": 1643.2637555172578 + }, + "post_job_actions": { + "HideDatasetActionoutput_param_text": { + "action_arguments": {}, + "action_type": "HideDatasetAction", + "output_name": "output_param_text" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "5ac8a4bf7a8d", + "name": "map_param_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"input_param_type\": {\"type\": \"text\", \"__current_case__\": 0, \"input_param\": {\"__class__\": \"ConnectedValue\"}, \"mappings\": [{\"__index__\": 0, \"from\": \"stranded - 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"id": 14, + "id": 17, "input_connections": { "input_param_type|input_param": { - "id": 4, + "id": 7, "output_name": "output" } }, @@ -613,7 +739,7 @@ } ], "position": { - "left": 790.5858684328869, + "left": 867.4070007672439, "top": 1993.6777444451404 }, "post_job_actions": { @@ -637,22 +763,22 @@ "when": null, "workflow_outputs": [] }, - "15": { + "18": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, - "id": 15, + "id": 18, "input_connections": { "refGenomeSource|GTFconditional|genomeDir": { - "id": 2, + "id": 4, "output_name": "output" }, "refGenomeSource|GTFconditional|sjdbGTFfile": { - "id": 3, + "id": 5, "output_name": "output" }, "singlePaired|input": { - "id": 10, + "id": 12, "output_name": "out_pairs" } }, @@ -699,7 +825,7 @@ } ], "position": { - "left": 647.1523155953676, + "left": 723.9734479297246, "top": 586.9799136582777 }, "post_job_actions": { @@ -763,857 +889,669 @@ } ] }, - "16": { + "19": { "annotation": "", - "id": 16, + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", + "errors": null, + "id": 19, "input_connections": { - "RNA STAR count tables": { - "id": 15, - "input_subworkflow_step_id": 4, - "output_name": "reads_per_gene" + "alignment": { + "id": 18, + "output_name": "mapped_reads" }, - "Sample table to add tags": { - "id": 6, - "input_subworkflow_step_id": 2, + "anno|reference_gene_sets": { + "id": 5, "output_name": "output" }, - "Strandness param": { - "id": 4, - "input_subworkflow_step_id": 3, + "strand_specificity": { + "id": 15, + "output_name": "output_param_text" + }, + "when": { + "id": 6, "output_name": "output" } }, - "inputs": [], + "inputs": [ + { + "description": "runtime parameter for tool featureCounts", + "name": "anno" + } + ], "label": null, - "name": "Process Count files", - "outputs": [], - "position": { - "left": 1875.6228149071408, - "top": 962.4763887841759 - }, - "subworkflow": { - "a_galaxy_workflow": "true", - "annotation": "", - 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"21": { + "25": { "annotation": "", - "id": 21, + "id": 25, "input_connections": { "Cutadapt Reports": { - "id": 10, + "id": 12, "input_subworkflow_step_id": 2, "output_name": "report" }, "FASTQ collection": { - "id": 11, + "id": 13, "input_subworkflow_step_id": 0, "output_name": "output" }, "STAR logs": { - "id": 15, + "id": 18, "input_subworkflow_step_id": 3, "output_name": "output_log" }, "STAR paired-end BAM": { - "id": 15, + "id": 18, "input_subworkflow_step_id": 5, "output_name": "mapped_reads" }, "featureCounts summaries": { - "id": 16, + "id": 24, "input_subworkflow_step_id": 1, "output_name": "FeatureCounts Summary Table" }, "reference_annotation_gtf": { - "id": 3, + "id": 5, "input_subworkflow_step_id": 4, "output_name": "output" }, "when": { - "id": 1, + "id": 3, "output_name": "output" } }, @@ -2587,7 +2773,7 @@ "name": "RNA-seq-Paired-QC", "outputs": [], "position": { - "left": 2581.8385293658202, + "left": 2658.6596617001774, "top": 574.7767421741249 }, "subworkflow": { @@ -3199,26 +3385,22 @@ } ] }, - "22": { + "26": { "annotation": "Count files have a header if featureCounts is used.", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", "errors": null, - "id": 22, + "id": 26, "input_connections": { - "batch_factors": { - "id": 9, + "header": { + "id": 6, "output_name": "output" }, "select_data|countsFile": { - "id": 16, + "id": 24, "output_name": "Tagged Count Tables" } }, "inputs": [ - { - "description": "runtime parameter for tool DESeq2", - "name": "batch_factors" - }, { "description": "runtime parameter for tool DESeq2", "name": "select_data" @@ -3237,7 +3419,7 @@ } ], "position": { - "left": 2566.26663539139, + "left": 2643.087767725747, "top": 1017.2514257011151 }, "post_job_actions": { @@ -3263,21 +3445,21 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"RuntimeValue\"}, \"header\": false, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"ConnectedValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.11.40.7+galaxy2", "type": "tool", "uuid": "9436d70d-95ee-46a6-86c3-60294c3a6967", "when": null, "workflow_outputs": [ - { - "label": "Differential Expression Analysis using DESeq2", - "output_name": "deseq_out", - "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" - }, { "label": "DESeq2 Plots", "output_name": "plots", "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" + }, + { + "label": "Differential Expression Analysis using DESeq2", + "output_name": "deseq_out", + "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" } ] } @@ -3285,6 +3467,6 @@ "tags": [ "RNAseq" ], - "uuid": "c85f7231-8058-4809-b83b-bc4d079c3b61", - "version": 1 + "uuid": "ef774348-5194-42f4-a7f2-854b6a082147", + "version": 11 } \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/test-data/Sample table.tabular b/workflows/transcriptomics/rnaseq-pe/test-data/Sample table.tabular deleted file mode 100644 index 053ee24ca..000000000 --- a/workflows/transcriptomics/rnaseq-pe/test-data/Sample table.tabular +++ /dev/null @@ -1,4 +0,0 @@ -GSM461181 treat paired -GSM461180 treat paired -GSM461178 untreat paired -GSM461177 untreat paired From 4d628aefcbf40b6432afee18201a3dd85ed7fdbf Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Thu, 24 Oct 2024 19:53:08 +0200 Subject: [PATCH 35/47] update test asserts --- .../rnaseq-pe/rnaseq-pe-tests.yml | 120 +++++++++--------- 1 file changed, 60 insertions(+), 60 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 395a5d20b..03970ec36 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -65,12 +65,12 @@ MultiQC stats: asserts: has_text_matching: - expression: "GSM461177\t0.04[0-9]*\t80.94[0-9]*\t0.61[0-9]*\t0.05[0-9]*\t0.04[0-9]*\t99.32[0-9]*\t0.04[0-9]*\t95.98\t0.00[0-9]*\t1.86[0-9]*" - expression: "GSM461177_forward\t\t\t\t\t\t\t\t\t\t\t27.95[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" - expression: "GSM461177_reverse\t\t\t\t\t\t\t\t\t\t\t28.22[0-9]*\t44.0\t37.0\t37\t10.0\t0.05[0-9]*" - expression: "GSM461180\t0.03[0-9]*\t81.41[0-9]*\t1.64[0-9]*\t0.04[0-9]*\t0.04[0-9]*\t97.94\t0.04[0-9]*\t94.84\t0.00[0-9]*\t13.51[0-9]*" - expression: "GSM461180_forward\t\t\t\t\t\t\t\t\t\t\t23.85[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" - expression: "GSM461180_reverse\t\t\t\t\t\t\t\t\t\t\t12.44[0-9]*\t45.0\t37.0\t37\t10.0\t0.04[0-9]*" + expression: "SRR5085167 0.101987 16.162911216271468 43.6174 0.333609 0.311683 93.43 0.11384799999999999 34.13 0.19783499999999998 44.157520246189655 " + expression: "SRR5085167_forward 36.3353936353624 46.0 75.0 75 27.27272727272727 0.398717" + expression: "SRR5085167_reverse 35.311326379081535 46.0 75.0 75 45.45454545454545 0.398717" + expression: "SRR5085169 0.193065 16.864768257390264 45.1412 0.618435 0.573608 92.75 0.21743099999999999 35.16 0.35617699999999997 44.442394599268845 " + expression: "SRR5085169_forward 38.42011496346503 46.0 75.0 75 18.181818181818183 0.736641" + expression: "SRR5085169_reverse 37.05721627112811 45.0 75.0 75 36.36363636363637 0.736641" DESeq2 Plots: has_size: size: 33420 @@ -78,165 +78,165 @@ Differential Expression Analysis using DESeq2: asserts: has_text_matching: - expression: "FBgn0025740\t333.11[0-9]*\t-0.33[0-9]*\t0.11[0-9]*\t-2.88[0-9]*\t0.00[0-9]*\t0.39[0-9]*" - expression: "FBgn0039923\t411.66[0-9]*\t-0.10[0-9]*\t0.10[0-9]*\t-0.95[0-9]*\t0.33[0-9]*\t0.99[0-9]*" + expression: "YML123C 122.984408142053 -1.67239392201746 0.218248491337382 -7.66279717110243 1.81926543236553e-14 5.04118451308489e-11" + expression: "YAL038W 1992.92679845592 -0.241941432622694 0.0736976375169541 -3.28289265130155 0.00102747784078829 0.177946318551521" Stranded Coverage: element_tests: SRR5085167_forward: has_size: - value: 3058282 - delta: 150000 + value: 635210 + delta: 30000 SRR5085168_forward: has_size: - value: 3058282 - delta: 150000 + value: 768801 + delta: 35000 SRR5085169_forward: has_size: - value: 3058282 - delta: 150000 + value: 1007711 + delta: 50000 SRR5085170_forward: has_size: - value: 3058282 - delta: 150000 + value: 730506 + delta: 35000 SRR5085167_reverse: has_size: - value: 3058282 - delta: 150000 + value: 618578 + delta: 30000 SRR5085168_reverse: has_size: - value: 3058282 - delta: 150000 + value: 746428 + delta: 35000 SRR5085169_reverse: has_size: - value: 3058282 - delta: 150000 + value: 982336 + delta: 50000 SRR5085170_reverse: has_size: - value: 3058282 - delta: 150000 + value: 717853 + delta: 35000 Gene Abundance Estimates from StringTie: element_tests: SRR5085167: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + expression: "YAL038W CDC19 chrI + 71786 73288 91.357285 3187.555420 3870.161377" SRR5085168: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + expression: "YAL038W CDC19 chrI + 71786 73288 123.424103 3796.197510 5242.119629" SRR5085169: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + expression: "YAL038W CDC19 chrI + 71786 73288 162.956757 3145.118408 5248.983887" SRR5085170: asserts: has_text_matching: - expression: "FBgn0017545\tRpS3A\tchr4\t-\t65225\t67207\t324.32[0-9]*\t135844.57[0-9]*\t364040.59[0-9]*" + expression: "YAL038W CDC19 chrI + 71786 73288 97.684654 2767.013672 4343.708496" Unstranded Coverage: element_tests: SRR5085167: has_size: - value: 3058282 - delta: 150000 + value: 1140004 + delta: 50000 SRR5085168: has_size: - value: 3058282 - delta: 150000 + value: 1399098 + delta: 70000 SRR5085169: has_size: - value: 3058282 - delta: 150000 + value: 1875151 + delta: 90000 SRR5085170: has_size: - value: 3058282 - delta: 150000 + value: 1324555 + delta: 60000 Mapped Reads: element_tests: SRR5085167: has_size: - value: 3058282 - delta: 150000 + value: 56913572 + delta: 2500000 SRR5085168: has_size: - value: 3058282 - delta: 150000 + value: 63050829 + delta: 3000000 SRR5085169: has_size: - value: 3058282 - delta: 150000 + value: 102904084 + delta: 5000000 SRR5085170: has_size: - value: 3058282 - delta: 150000 + value: 69944408 + delta: 3500000 Genes Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3376.27 3155.33 3597.21 OK" SRR5085168: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3897.89 3661.55 4134.23 OK" SRR5085169: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3250.26 3067.67 3432.84 OK" SRR5085170: asserts: has_line: - line: "FBtr0089175 - - FBgn0017545 RpS3A - chr4:66196-67207 910 409.883 114524 108672 120376 OK" + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 2919.15 2731.02 3107.28 OK" Transcripts Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 102.307 3376.27 3155.33 3597.21 OK" SRR5085168: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 138.338 3897.89 3661.55 4134.23 OK" SRR5085169: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 184.37 3250.26 3067.67 3432.84 OK" SRR5085170: asserts: has_line: - line: "FBgn0017545 - - FBgn0017545 RpS3A - chr4:65224-67207 - - 128511 122676 134345 OK" + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 111.49 2919.15 2731.02 3107.28 OK" Tagged Count Tables: element_tests: SRR5085167: asserts: has_line: - line: "FBgn0017545 6109" + line: "YAL038W 1609" SRR5085168: asserts: has_line: - line: "FBgn0017545 6109" + line: "YAL038W 2118" SRR5085169: asserts: has_line: - line: "FBgn0017545 6109" + line: "YAL038W 2854" SRR5085170: asserts: has_line: - line: "FBgn0017545 6109" + line: "YAL038W 1688" FeatureCounts Summary Table: element_tests: SRR5085167: asserts: has_line: - line: "Assigned 45715" + line: "Assigned 101987" SRR5085168: asserts: has_line: - line: "Assigned 45715" + line: "Assigned 130707" SRR5085169: asserts: has_line: - line: "Assigned 45715" + line: "Assigned 193065" SRR5085170: asserts: has_line: - line: "Assigned 45715" \ No newline at end of file + line: "Assigned 120275" \ No newline at end of file From 121278613d7e0c6991009150bcc5e6608836e21b Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Fri, 25 Oct 2024 15:41:27 +0200 Subject: [PATCH 36/47] Remove DESeq2 step --- .../rnaseq-pe/rnaseq-pe-tests.yml | 118 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 1107 +++++++---------- 2 files changed, 459 insertions(+), 766 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 03970ec36..67870c3b4 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -4,10 +4,6 @@ class: File location: https://zenodo.org/records/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf filetype: gtf - Sample table: - class: File - location: https://zenodo.org/records/13987631/files/sample_table.tabular - filetype: tabular Collection paired FASTQ files: class: Collection collection_type: list:paired @@ -65,21 +61,15 @@ MultiQC stats: asserts: has_text_matching: - expression: "SRR5085167 0.101987 16.162911216271468 43.6174 0.333609 0.311683 93.43 0.11384799999999999 34.13 0.19783499999999998 44.157520246189655 " - expression: "SRR5085167_forward 36.3353936353624 46.0 75.0 75 27.27272727272727 0.398717" - expression: "SRR5085167_reverse 35.311326379081535 46.0 75.0 75 45.45454545454545 0.398717" - expression: "SRR5085169 0.193065 16.864768257390264 45.1412 0.618435 0.573608 92.75 0.21743099999999999 35.16 0.35617699999999997 44.442394599268845 " - expression: "SRR5085169_forward 38.42011496346503 46.0 75.0 75 18.181818181818183 0.736641" - expression: "SRR5085169_reverse 37.05721627112811 45.0 75.0 75 36.36363636363637 0.736641" - DESeq2 Plots: - has_size: - size: 33420 - delta: 1500 - Differential Expression Analysis using DESeq2: + expression: "SRR5085167\t0.10[0-9]*\t16.16[0-9]*\t43.61[0-9]*\t0.33[0-9]*\t0.31[0-9]*\t93.43\t0.11[0-9]*\t34.13\t0.19[0-9]*\t44.15[0-9]*\t\t\t\t\t\t" + expression: "SRR5085167_forward\t\t\t\t\t\t\t\t\t\t\t36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" + expression: "SRR5085167_reverse\t\t\t\t\t\t\t\t\t\t\t35.31[0-9]*\t46.0\t75.0\t75\t45.45[0-9]*\t0.39[0-9]*" asserts: has_text_matching: - expression: "YML123C 122.984408142053 -1.67239392201746 0.218248491337382 -7.66279717110243 1.81926543236553e-14 5.04118451308489e-11" - expression: "YAL038W 1992.92679845592 -0.241941432622694 0.0736976375169541 -3.28289265130155 0.00102747784078829 0.177946318551521" + expression: "SRR5085168\t0.13[0-9]*\t19.04[0-9]*\t39.25\t0.38[0-9]*\t0.35[0-9]*\t92.47[0-9]*\t0.14[0-9]*\t38.18\t0.20[0-9]*\t42.88[0-9]*\t\t\t\t\t\t" + expression: "SRR5085168_forward\t\t\t\t\t\t\t\t\t\t\t34.17[0-9]*\t45.0\t75.0\t75\t18.18[0-9]*\t0.45[0-9]*" + expression: "SRR5085168_reverse\t\t\t\t\t\t\t\t\t\t\t34.28[0-9]*\t45.0\t75.0\t75\t36.36[0-9]*\t0.45[0-9]*" + Stranded Coverage: element_tests: SRR5085167_forward: @@ -90,14 +80,6 @@ has_size: value: 768801 delta: 35000 - SRR5085169_forward: - has_size: - value: 1007711 - delta: 50000 - SRR5085170_forward: - has_size: - value: 730506 - delta: 35000 SRR5085167_reverse: has_size: value: 618578 @@ -106,32 +88,16 @@ has_size: value: 746428 delta: 35000 - SRR5085169_reverse: - has_size: - value: 982336 - delta: 50000 - SRR5085170_reverse: - has_size: - value: 717853 - delta: 35000 Gene Abundance Estimates from StringTie: element_tests: SRR5085167: asserts: has_text_matching: - expression: "YAL038W CDC19 chrI + 71786 73288 91.357285 3187.555420 3870.161377" + expression: "YAL038W\tCDC19\tchrI\t+\t71786\t73288\t91.35[0-9]*\t3187.55[0-9]*\t3870.16[0-9]*" SRR5085168: asserts: has_text_matching: - expression: "YAL038W CDC19 chrI + 71786 73288 123.424103 3796.197510 5242.119629" - SRR5085169: - asserts: - has_text_matching: - expression: "YAL038W CDC19 chrI + 71786 73288 162.956757 3145.118408 5248.983887" - SRR5085170: - asserts: - has_text_matching: - expression: "YAL038W CDC19 chrI + 71786 73288 97.684654 2767.013672 4343.708496" + expression: "YAL038W\tCDC19\tchrI\t+\t71786\t73288\t123.42[0-9]*\t3796.19[0-9]*\t5242.11[0-9]*" Unstranded Coverage: element_tests: SRR5085167: @@ -142,14 +108,6 @@ has_size: value: 1399098 delta: 70000 - SRR5085169: - has_size: - value: 1875151 - delta: 90000 - SRR5085170: - has_size: - value: 1324555 - delta: 60000 Mapped Reads: element_tests: SRR5085167: @@ -160,83 +118,43 @@ has_size: value: 63050829 delta: 3000000 - SRR5085169: - has_size: - value: 102904084 - delta: 5000000 - SRR5085170: - has_size: - value: 69944408 - delta: 3500000 Genes Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3376.27 3155.33 3597.21 OK" + line: "YAL038W\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t-\t-\t3376.27\t3155.33\t3597.21\tOK" SRR5085168: asserts: has_line: - line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3897.89 3661.55 4134.23 OK" - SRR5085169: - asserts: - has_line: - line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3250.26 3067.67 3432.84 OK" - SRR5085170: - asserts: - has_line: - line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 2919.15 2731.02 3107.28 OK" + line: "YAL038W\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t-\t-\t3897.89\t3661.55\t4134.23\tOK" Transcripts Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 102.307 3376.27 3155.33 3597.21 OK" + line: "YAL038W_mRNA\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t1503\t102.30[0-9]*\t3376.27\t3155.33\t3597.21\tOK" SRR5085168: asserts: has_line: - line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 138.338 3897.89 3661.55 4134.23 OK" - SRR5085169: - asserts: - has_line: - line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 184.37 3250.26 3067.67 3432.84 OK" - SRR5085170: - asserts: - has_line: - line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 111.49 2919.15 2731.02 3107.28 OK" - Tagged Count Tables: + line: "YAL038W_mRNA\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t1503\t138.33[0-9]*\t3897.89\t3661.55\t4134.23\tOK" + Counts Table: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W 1609" + line: "YAL038W\t1609" SRR5085168: asserts: has_line: - line: "YAL038W 2118" - SRR5085169: - asserts: - has_line: - line: "YAL038W 2854" - SRR5085170: - asserts: - has_line: - line: "YAL038W 1688" + line: "YAL038W\t2118" FeatureCounts Summary Table: element_tests: SRR5085167: asserts: has_line: - line: "Assigned 101987" + line: "Assigned\t101987" SRR5085168: asserts: has_line: - line: "Assigned 130707" - SRR5085169: - asserts: - has_line: - line: "Assigned 193065" - SRR5085170: - asserts: - has_line: - line: "Assigned 120275" \ No newline at end of file + line: "Assigned\t130707" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 073e5ce57..109a7d325 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,32 +1,12 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools. The differential expression analysis is performed using DESeq2.\n", + "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. Alternatively, featureCounts can be used to count the reads/fragments per gene. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.\n", "comments": [ { "child_steps": [ - 22, - 23 - ], - "color": "red", - "data": { - "title": "Coverage Files" - }, - "id": 2, - "position": [ - 2586.921132334357, - 0 - ], - "size": [ - 375, - 538 - ], - "type": "frame" - }, - { - "child_steps": [ + 14, 15, - 16, - 17 + 16 ], "color": "lime", "data": { @@ -35,7 +15,7 @@ "id": 0, "position": [ 847.321132334357, - 1592.6 + 1254.5 ], "size": [ 251, @@ -45,24 +25,44 @@ }, { "child_steps": [ - 14, - 20, - 21 + 13, + 21, + 22 ], "color": "yellow", "data": { "title": "Additional quantification" }, - "id": 1, + "id": 2, "position": [ 1383.0211323343572, - 1413.8 + 1075.6999999999998 ], "size": [ 860, 716 ], "type": "frame" + }, + { + "child_steps": [ + 18, + 19 + ], + "color": "red", + "data": { + "title": "Coverage Files" + }, + "id": 1, + "position": [ + 1621.4, + 0 + ], + "size": [ + 375, + 538 + ], + "type": "frame" } ], "creator": [ @@ -80,7 +80,7 @@ "format-version": "0.1", "license": "MIT", "release": "0.10", - "name": "rnaseq-pe", + "name": "RNAseq_PE", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -102,7 +102,7 @@ "outputs": [], "position": { "left": 0, - "top": 733.4300127682214 + "top": 395.3300127682214 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", @@ -114,7 +114,7 @@ { "label": null, "output_name": "output", - "uuid": "349d9805-89b8-4b7c-94ec-17f1bc19f2a0" + "uuid": "164bfd53-9a44-4ccc-b5cd-0579dafb1db8" } ] }, @@ -135,7 +135,7 @@ "outputs": [], "position": { "left": 43.382193674328164, - "top": 856.5124765005733 + "top": 518.4124765005732 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", @@ -147,7 +147,7 @@ { "label": null, "output_name": "output", - "uuid": "f43a77a2-f04a-4713-b1ab-04e9223ab8fa" + "uuid": "275f8ac7-87df-4a37-bb2a-15fa2fe85ad5" } ] }, @@ -168,7 +168,7 @@ "outputs": [], "position": { "left": 76.82113233435703, - "top": 1007.0008028213834 + "top": 668.9008028213834 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -195,7 +195,7 @@ "outputs": [], "position": { "left": 117.49850394573046, - "top": 1117.6931018245803 + "top": 779.5931018245802 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -207,7 +207,7 @@ { "label": null, "output_name": "output", - "uuid": "78e6bb9a-69af-449b-ad5f-7c1c8296bdaf" + "uuid": "a3d78ed2-e961-4d34-9a7e-68a6872c64ac" } ] }, @@ -228,7 +228,7 @@ "outputs": [], "position": { "left": 147.49847445771462, - "top": 1229.3288050461836 + "top": 891.2288050461835 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -240,7 +240,7 @@ { "label": null, "output_name": "output", - "uuid": "5778573f-950f-43eb-aa84-8e4191df8b0c" + "uuid": "b6a5f44e-06f4-4ac9-811b-40a2b48252c6" } ] }, @@ -261,7 +261,7 @@ "outputs": [], "position": { "left": 197.4984987055553, - "top": 1326.5006367761569 + "top": 988.4006367761568 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -288,7 +288,7 @@ "outputs": [], "position": { "left": 237.15865423690892, - "top": 1435.2340383001115 + "top": 1097.1340383001116 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -300,7 +300,7 @@ { "label": null, "output_name": "output", - "uuid": "0d981cb2-b09c-4fbc-a0cc-eded4a12a801" + "uuid": "f8a0a43f-d4b3-42ad-a565-82974ebc035f" } ] }, @@ -321,7 +321,7 @@ "outputs": [], "position": { "left": 280.70402093882234, - "top": 1570.8860110851008 + "top": 1232.7860110851007 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -333,7 +333,7 @@ { "label": null, "output_name": "output", - "uuid": "1b3d905c-be93-46ad-b58e-cdf5bbdbf6eb" + "uuid": "0f6c75c7-6c9b-4a75-ae8a-450ee390a843" } ] }, @@ -354,7 +354,7 @@ "outputs": [], "position": { "left": 305.59290083057465, - "top": 1666.0254709507822 + "top": 1327.9254709507823 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -366,42 +366,15 @@ { "label": null, "output_name": "output", - "uuid": "8e9a31f7-0da5-4aae-8ec8-54bc28fbb979" + "uuid": "38a0fd86-4369-4f85-9f42-911b6e478b4a" } ] }, "9": { - "annotation": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "content_id": null, - "errors": null, - "id": 9, - "input_connections": {}, - "inputs": [ - { - "description": "Provide experimental and batch details. This is tabular containing all the sample names in the first column. There must be a column with primary factor/experimental information. There might be additional columns with one batch information each.", - "name": "Sample table" - } - ], - "label": "Sample table", - "name": "Input dataset", - "outputs": [], - "position": { - "left": 1538.9856847149777, - "top": 909.2581294996864 - }, - "tool_id": null, - "tool_state": "{\"optional\": false, \"format\": [\"tabular\"], \"tag\": null}", - "tool_version": null, - "type": "data_input", - "uuid": "a4a04f75-7bb7-48c2-8a8f-b692b62c4252", - "when": null, - "workflow_outputs": [] - }, - "10": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", "content_id": null, "errors": null, - "id": 10, + "id": 9, "input_connections": {}, "inputs": [ { @@ -414,7 +387,7 @@ "outputs": [], "position": { "left": 336.93486951390355, - "top": 1784.313630812311 + "top": 1446.2136308123108 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -426,15 +399,15 @@ { "label": null, "output_name": "output", - "uuid": "5b5095cc-6934-4336-9321-028436a11344" + "uuid": "b9385caf-799d-4e0e-a1e6-97868d2233ea" } ] }, - "11": { + "10": { "annotation": "Whether FPKM values should be computed with StringTie", "content_id": null, "errors": null, - "id": 11, + "id": 10, "input_connections": {}, "inputs": [ { @@ -447,7 +420,7 @@ "outputs": [], "position": { "left": 345.60201891969245, - "top": 1905.5010561327158 + "top": 1567.401056132716 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -459,15 +432,15 @@ { "label": null, "output_name": "output", - "uuid": "5b7df78b-f88d-4ef5-9e70-938adcf11bfa" + "uuid": "8dd69bcb-492c-4566-9cd7-50caaa30aa7f" } ] }, - "12": { + "11": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 12, + "id": 11, "input_connections": { "library|input_1": { "id": 2, @@ -502,7 +475,7 @@ ], "position": { "left": 374.33462420145804, - "top": 607.862671571285 + "top": 269.76267157128495 }, "post_job_actions": { "HideDatasetActionout1": { @@ -535,11 +508,11 @@ "when": null, "workflow_outputs": [] }, - "13": { + "12": { "annotation": "", "content_id": "__FLATTEN__", "errors": null, - "id": 13, + "id": 12, "input_connections": { "input": { "id": 2, @@ -557,7 +530,7 @@ ], "position": { "left": 422.58362558810336, - "top": 963.9873433527641 + "top": 625.8873433527641 }, "post_job_actions": {}, "tool_id": "__FLATTEN__", @@ -568,11 +541,11 @@ "when": null, "workflow_outputs": [] }, - "14": { + "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", "errors": null, - "id": 14, + "id": 13, "input_connections": { "components_0|param_type|component_value": { "id": 4, @@ -590,7 +563,7 @@ ], "position": { "left": 1489.6076401751156, - "top": 1513.204961480357 + "top": 1175.104961480357 }, "post_job_actions": { "HideDatasetActionout1": { @@ -613,11 +586,11 @@ "when": null, "workflow_outputs": [] }, - "15": { + "14": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 15, + "id": 14, "input_connections": { "input_param_type|input_param": { "id": 7, @@ -640,7 +613,7 @@ ], "position": { "left": 871.929384855411, - "top": 1643.2637555172578 + "top": 1305.1637555172579 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -663,11 +636,11 @@ "when": null, "workflow_outputs": [] }, - "16": { + "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 16, + "id": 15, "input_connections": { "input_param_type|input_param": { "id": 7, @@ -690,7 +663,7 @@ ], "position": { "left": 872.1470350742542, - "top": 1823.4515528952898 + "top": 1485.3515528952898 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -713,11 +686,11 @@ "when": null, "workflow_outputs": [] }, - "17": { + "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.2.0", "errors": null, - "id": 17, + "id": 16, "input_connections": { "input_param_type|input_param": { "id": 7, @@ -740,7 +713,7 @@ ], "position": { "left": 867.4070007672439, - "top": 1993.6777444451404 + "top": 1655.5777444451405 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -763,11 +736,11 @@ "when": null, "workflow_outputs": [] }, - "18": { + "17": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1", "errors": null, - "id": 18, + "id": 17, "input_connections": { "refGenomeSource|GTFconditional|genomeDir": { "id": 4, @@ -778,7 +751,7 @@ "output_name": "output" }, "singlePaired|input": { - "id": 12, + "id": 11, "output_name": "out_pairs" } }, @@ -826,7 +799,7 @@ ], "position": { "left": 723.9734479297246, - "top": 586.9799136582777 + "top": 248.8799136582777 }, "post_job_actions": { "HideDatasetActionsignal_unique_str1": { @@ 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{\"paired_end_status\": \"PE_fragments\", \"__current_case__\": 2, \"check_distance_enabled\": {\"checkFragLength\": \"false\", \"__current_case__\": 1}, \"only_both_ends\": false, \"exclude_chimerics\": true}, \"read_filtering_parameters\": {\"mapping_quality\": \"0\", \"splitonly\": \"\", \"primary\": false, \"ignore_dup\": false}, \"strand_specificity\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.0.3+galaxy2", - "type": "tool", - "uuid": "5a03b546-eb3f-4e99-b845-24c8f54ed183", - "when": "$(inputs.when)", - "workflow_outputs": [] - }, - "20": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0", - "errors": null, - "id": 20, - "input_connections": { - "guide|guide_source|ref_hist": { - "id": 5, - "output_name": "output" - }, - "input_options|input_bam": { - "id": 18, - "output_name": "mapped_reads" - }, - "rna_strandness": { - "id": 17, - "output_name": 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"id": 8, + "id": 6, "input_connections": { "input_param_type|input_param": { - "id": 3, + "id": 2, "output_name": "output" } }, @@ -2472,7 +2362,7 @@ } ], "position": { - "left": 282.1421709032883, + "left": 279.9999833196541, "top": 401.33828843669767 }, "post_job_actions": { @@ -2496,18 +2386,18 @@ "when": null, "workflow_outputs": [] }, - "9": { + "7": { "annotation": "featureCounts summaries", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, - "id": 9, + "id": 7, "input_connections": { "style_cond|type_cond|pick_from_0|value": { "id": 1, "output_name": "output" }, "style_cond|type_cond|pick_from_1|value": { - "id": 6, + "id": 5, "output_name": "output" } }, @@ -2521,8 +2411,8 @@ } ], "position": { - "left": 842.1422267022583, - "top": 16.0 + "left": 840.0000391186242, + "top": 16 }, "post_job_actions": { "RenameDatasetActiondata_param": { @@ -2553,18 +2443,18 @@ } ] }, - "10": { + "8": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1", "errors": null, - 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"id": 13, + "id": 12, "input_subworkflow_step_id": 0, "output_name": "output" }, "STAR logs": { - "id": 18, + "id": 17, "input_subworkflow_step_id": 3, "output_name": "output_log" }, "STAR paired-end BAM": { - "id": 18, + "id": 17, "input_subworkflow_step_id": 5, "output_name": "mapped_reads" }, "featureCounts summaries": { - "id": 24, + "id": 23, "input_subworkflow_step_id": 1, "output_name": "FeatureCounts Summary Table" }, @@ -2773,8 +2626,8 @@ "name": "RNA-seq-Paired-QC", "outputs": [], "position": { - "left": 2658.6596617001774, - "top": 574.7767421741249 + "left": 2527.234117718266, + "top": 628.3664416590253 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3384,89 +3237,11 @@ "uuid": "43ed1ffc-7df8-42a6-95f7-dc2b2060a910" } ] - }, - "26": { - "annotation": "Count files have a header if featureCounts is used.", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2", - "errors": null, - "id": 26, - "input_connections": { - "header": { - "id": 6, - "output_name": "output" - 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"name": "deseq2", - "owner": "iuc", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"advanced_options\": {\"esf\": \"\", \"fit_type\": \"1\", \"outlier_replace_off\": false, \"outlier_filter_off\": false, \"auto_mean_filter_off\": false, \"prefilter_conditional\": {\"prefilter\": \"\", \"__current_case__\": 1}}, \"batch_factors\": {\"__class__\": \"ConnectedValue\"}, \"header\": {\"__class__\": \"ConnectedValue\"}, \"output_options\": {\"output_selector\": \"pdf\", \"alpha_ma\": \"0.1\"}, \"select_data\": {\"how\": \"group_tags\", \"__current_case__\": 0, \"countsFile\": {\"__class__\": \"ConnectedValue\"}, \"rep_factorName\": [{\"__index__\": 0, \"factorName\": {\"__class__\": \"RuntimeValue\"}, \"rep_factorLevel\": [{\"__index__\": 0, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}, {\"__index__\": 1, \"factorLevel\": {\"__class__\": \"RuntimeValue\"}, \"groups\": {\"__class__\": \"RuntimeValue\"}}]}]}, \"tximport\": {\"tximport_selector\": \"count\", \"__current_case__\": 1}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.11.40.7+galaxy2", - "type": "tool", - "uuid": "9436d70d-95ee-46a6-86c3-60294c3a6967", - "when": null, - "workflow_outputs": [ - { - "label": "DESeq2 Plots", - "output_name": "plots", - "uuid": "bb56b400-7039-4547-9bcc-b3e028993d04" - }, - { - "label": "Differential Expression Analysis using DESeq2", - "output_name": "deseq_out", - "uuid": "6880e71b-da23-4131-a367-c6655cbe5371" - } - ] } }, "tags": [ "RNAseq" ], - "uuid": "ef774348-5194-42f4-a7f2-854b6a082147", - "version": 11 + "uuid": "e21c4a06-b5ec-4691-8511-c5ffb12ac8f4", + "version": 16 } \ No newline at end of file From 4f65c0500ab50866ed8830f6af7de9dce2b53761 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Sat, 26 Oct 2024 11:15:55 +0200 Subject: [PATCH 37/47] use only one sample, update readme, dockstore and changelog --- .../transcriptomics/rnaseq-pe/.dockstore.yml | 2 + .../transcriptomics/rnaseq-pe/CHANGELOG.md | 6 +- workflows/transcriptomics/rnaseq-pe/README.md | 19 +- .../rnaseq-pe/rnaseq-pe-tests.yml | 90 +--- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 407 ++++++++---------- 5 files changed, 197 insertions(+), 327 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/.dockstore.yml b/workflows/transcriptomics/rnaseq-pe/.dockstore.yml index c035638a3..a4081dbf2 100644 --- a/workflows/transcriptomics/rnaseq-pe/.dockstore.yml +++ b/workflows/transcriptomics/rnaseq-pe/.dockstore.yml @@ -9,3 +9,5 @@ workflows: authors: - name: Lucille Delisle orcid: 0000-0002-1964-4960 + - name: Pavankumar Videm + orcid: 0000-0002-5192-126X diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 0345757ab..95251a078 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -3,9 +3,9 @@ ## [0.10] 2024-09-23 ### Manual update -- Using a new subsampled test data from Zenodo record https://zenodo.org/records/13951092 -- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, Picard reports -- Added DESeq2 step that uses tags to choose factors +- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/4541751 +- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, featureCounts and Picard reports +- Added featureCounts as an alternative way to generate count files ## [0.9] 2024-09-23 diff --git a/workflows/transcriptomics/rnaseq-pe/README.md b/workflows/transcriptomics/rnaseq-pe/README.md index 3640d4976..93489bf62 100644 --- a/workflows/transcriptomics/rnaseq-pe/README.md +++ b/workflows/transcriptomics/rnaseq-pe/README.md @@ -2,9 +2,9 @@ ## Inputs dataset -- The workflow needs a list of dataset pairs of fastqsanger. -- As well as a gtf file with genes -- Optional, but recommended: a gtf file with regions to exclude from normalization in Cufflinks. +- Collection paired FASTQ files: The workflow needs a list of dataset pairs of fastqsanger. +- GTF file of annotation: A gtf file with genes annotation. +- GTF with regions to exclude from FPKM normalization with Cufflinks: Optional, but recommended. A gtf file with regions to exclude from normalization in Cufflinks. - For instance a gtf that masks chrM for the mm10 genome: @@ -15,16 +15,19 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM ## Inputs values -- adapter sequences: this depends on the library preparation. Usually classical Illumina RNA libraries are Truseq and ISML (relatively new Illumina library) is Nextera. If you don't know, use FastQC to determine if it is Truseq or Nextera. If the read length is relatively short (50bp), there is probably no adapter so it will not impact your results. -- reference_genome: this field will be adapted to the genomes available for STAR -- strandedness: For stranded RNA, reverse means that the first read in a pair is complementary to the coding sequence, forward means that the first read in a pair is in the same orientation as the coding sequence. This will only count alignments that are compatible with your library preparation strategy. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. -- cufflinks_FPKM: Whether you want to get FPKM with Cufflinks (pretty long) -- stringtie_FPKM: Whether you want to get FPKM/TPM etc... with StringTie. +- Forward and Reverse adapter: this depends on the library preparation. Usually classical Illumina RNA libraries are Truseq and ISML (relatively new Illumina library) is Nextera. If you don't know, use FastQC to determine if it is Truseq or Nextera. If the read length is relatively short (50bp), there is probably no adapter so it will not impact your results. +- Generate QC reports: whether to generate an aggrigated MultiQC report from FastQC, Cutadapt, STAR, featureCounts and Picard. +- Reference genome: this field will be adapted to the genomes available for STAR. +- Strandedness: For stranded RNA, reverse means that the first read in a pair is complementary to the coding sequence, forward means that the first read in a pair is in the same orientation as the coding sequence. This will only count alignments that are compatible with your library preparation strategy. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. +- Use featureCounts for generating count tables: Whether to use count tables from featureCounts instead of from STAR. +- Compute Cufflinks FPKM: Whether you want to get FPKM with Cufflinks (pretty long). +- Compute StringTie FPKM: Whether you want to get FPKM/TPM etc... with StringTie. ## Processing - The workflow will remove adapters and low quality bases and filter out any read smaller than 15bp. - The filtered reads are mapped with STAR with ENCODE parameters (for long RNA-seq but I use it for short also). STAR is also used to count reads per gene and generate strand-specific normalized coverage (on uniquely mapped reads). +- Optionally featureCounts is used to generate count files when this option enabled. - A multiQC is run to have an overview of the QC. This can also be used to get the strandedness. - FPKM values for genes and transcripts are computed with cufflinks using correction for multi-mapped reads (this step is optionnal). - FPKM/TPM values for genes are computed with StringTie. diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 67870c3b4..12b0702ae 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -18,45 +18,15 @@ - class: File identifier: reverse location: https://zenodo.org/records/13987631/files/SRR5085167_reverse.fastqsanger.gz - - class: Collection - type: paired - identifier: SRR5085168 - elements: - - class: File - identifier: forward - location: https://zenodo.org/records/13987631/files/SRR5085168_forward.fastqsanger.gz - - class: File - identifier: reverse - location: https://zenodo.org/records/13987631/files/SRR5085168_reverse.fastqsanger.gz - - class: Collection - type: paired - identifier: SRR5085169 - elements: - - class: File - identifier: forward - location: https://zenodo.org/records/13987631/files/SRR5085169_forward.fastqsanger.gz - - class: File - identifier: reverse - location: https://zenodo.org/records/13987631/files/SRR5085169_reverse.fastqsanger.gz - - class: Collection - type: paired - identifier: SRR5085170 - elements: - - class: File - identifier: forward - location: https://zenodo.org/records/13987631/files/SRR5085170_forward.fastqsanger.gz - - class: File - identifier: reverse - location: https://zenodo.org/records/13987631/files/SRR5085170_reverse.fastqsanger.gz Forward adapter: AGATCGGAAGAG Reverse adapter: GATCGTCGGACT - Generate QC reports?: true + Generate QC reports: true Reference genome: sacCer3 Use featureCounts for generating count tables: true - strandedness: stranded - forward - Compute Cufflinks FPKM?: true + Strandedness: stranded - forward + Compute Cufflinks FPKM: true GTF with regions to exclude from FPKM normalization with Cufflinks: null - Compute StringTie FPKM?: true + Compute StringTie FPKM: true outputs: MultiQC stats: asserts: @@ -64,97 +34,55 @@ expression: "SRR5085167\t0.10[0-9]*\t16.16[0-9]*\t43.61[0-9]*\t0.33[0-9]*\t0.31[0-9]*\t93.43\t0.11[0-9]*\t34.13\t0.19[0-9]*\t44.15[0-9]*\t\t\t\t\t\t" expression: "SRR5085167_forward\t\t\t\t\t\t\t\t\t\t\t36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" expression: "SRR5085167_reverse\t\t\t\t\t\t\t\t\t\t\t35.31[0-9]*\t46.0\t75.0\t75\t45.45[0-9]*\t0.39[0-9]*" - asserts: - has_text_matching: - expression: "SRR5085168\t0.13[0-9]*\t19.04[0-9]*\t39.25\t0.38[0-9]*\t0.35[0-9]*\t92.47[0-9]*\t0.14[0-9]*\t38.18\t0.20[0-9]*\t42.88[0-9]*\t\t\t\t\t\t" - expression: "SRR5085168_forward\t\t\t\t\t\t\t\t\t\t\t34.17[0-9]*\t45.0\t75.0\t75\t18.18[0-9]*\t0.45[0-9]*" - expression: "SRR5085168_reverse\t\t\t\t\t\t\t\t\t\t\t34.28[0-9]*\t45.0\t75.0\t75\t36.36[0-9]*\t0.45[0-9]*" - Stranded Coverage: element_tests: SRR5085167_forward: has_size: value: 635210 delta: 30000 - SRR5085168_forward: - has_size: - value: 768801 - delta: 35000 SRR5085167_reverse: has_size: value: 618578 delta: 30000 - SRR5085168_reverse: - has_size: - value: 746428 - delta: 35000 Gene Abundance Estimates from StringTie: element_tests: SRR5085167: asserts: has_text_matching: - expression: "YAL038W\tCDC19\tchrI\t+\t71786\t73288\t91.35[0-9]*\t3187.55[0-9]*\t3870.16[0-9]*" - SRR5085168: - asserts: - has_text_matching: - expression: "YAL038W\tCDC19\tchrI\t+\t71786\t73288\t123.42[0-9]*\t3796.19[0-9]*\t5242.11[0-9]*" + expression: "YAL038W\tCDC19\tchrI\t\\+\t71786\t73288\t91.35[0-9]*\t3187.55[0-9]*\t3870.16[0-9]*" Unstranded Coverage: element_tests: SRR5085167: has_size: value: 1140004 delta: 50000 - SRR5085168: - has_size: - value: 1399098 - delta: 70000 Mapped Reads: element_tests: SRR5085167: has_size: value: 56913572 delta: 2500000 - SRR5085168: - has_size: - value: 63050829 - delta: 3000000 Genes Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t-\t-\t3376.27\t3155.33\t3597.21\tOK" - SRR5085168: - asserts: - has_line: - line: "YAL038W\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t-\t-\t3897.89\t3661.55\t4134.23\tOK" + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3376.27 3155.33 3597.21 OK" Transcripts Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W_mRNA\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t1503\t102.30[0-9]*\t3376.27\t3155.33\t3597.21\tOK" - SRR5085168: - asserts: - has_line: - line: "YAL038W_mRNA\t-\t-\tYAL038W\tCDC19\t-\tchrI:71785-73288\t1503\t138.33[0-9]*\t3897.89\t3661.55\t4134.23\tOK" + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 102.307 3376.27 3155.33 3597.21 OK" Counts Table: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W\t1609" - SRR5085168: - asserts: - has_line: - line: "YAL038W\t2118" + line: "YAL038W 1609" FeatureCounts Summary Table: element_tests: SRR5085167: asserts: has_line: - line: "Assigned\t101987" - SRR5085168: - asserts: - has_line: - line: "Assigned\t130707" \ No newline at end of file + line: "Assigned 101987" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 109a7d325..0d3b09c6b 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -4,43 +4,43 @@ "comments": [ { "child_steps": [ - 14, - 15, - 16 + 13, + 21, + 22 ], - "color": "lime", + "color": "yellow", "data": { - "title": "Map Strandedness parameter" + "title": "Additional quantification" }, - "id": 0, + "id": 2, "position": [ - 847.321132334357, - 1254.5 + 1391.2086321940171, + 1073.6999999999998 ], "size": [ - 251, - 558 + 860, + 716 ], "type": "frame" }, { "child_steps": [ - 13, - 21, - 22 + 14, + 15, + 16 ], - "color": "yellow", + "color": "lime", "data": { - "title": "Additional quantification" + "title": "Map Strandedness parameter" }, - "id": 2, + "id": 0, "position": [ - 1383.0211323343572, - 1075.6999999999998 + 855.5086321940169, + 1252.5 ], "size": [ - 860, - 716 + 251, + 558 ], "type": "frame" }, @@ -55,7 +55,7 @@ }, "id": 1, "position": [ - 1621.4, + 1603.68749985966, 0 ], "size": [ @@ -86,95 +86,83 @@ }, "steps": { "0": { - "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "annotation": "Should be a list of paired-end RNA-seq fastqs", "content_id": null, "errors": null, "id": 0, "input_connections": {}, "inputs": [ { - "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", - "name": "Forward adapter" + "description": "Should be a list of paired-end RNA-seq fastqs", + "name": "Collection paired FASTQ files" } ], - "label": "Forward adapter", - "name": "Input parameter", + "label": "Collection paired FASTQ files", + "name": "Input dataset collection", "outputs": [], "position": { - "left": 0, - "top": 395.3300127682214 + "left": 0.0, + "top": 462.87500890145213 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", "tool_version": null, - "type": "parameter_input", - "uuid": "6d1de206-97c4-41ba-8702-a980f748a689", + "type": "data_collection_input", + "uuid": "020f7580-f647-471f-b210-dbf9dfcf80bf", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "164bfd53-9a44-4ccc-b5cd-0579dafb1db8" - } - ] + "workflow_outputs": [] }, "1": { - "annotation": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", - "name": "Reverse adapter" + "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "name": "Forward adapter" } ], - "label": "Reverse adapter", + "label": "Forward adapter", "name": "Input parameter", "outputs": [], "position": { - "left": 43.382193674328164, - "top": 518.4124765005732 + "left": 35.17186494140515, + "top": 567.328103383874 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "7aae38b8-39a8-4fba-bc6b-bda8c1ea9162", + "uuid": "6d1de206-97c4-41ba-8702-a980f748a689", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "275f8ac7-87df-4a37-bb2a-15fa2fe85ad5" - } - ] + "workflow_outputs": [] }, "2": { - "annotation": "Should be a list of paired-end RNA-seq fastqs", + "annotation": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Should be a list of paired-end RNA-seq fastqs", - "name": "Collection paired FASTQ files" + "description": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "name": "Reverse adapter" } ], - "label": "Collection paired FASTQ files", - "name": "Input dataset collection", + "label": "Reverse adapter", + "name": "Input parameter", "outputs": [], "position": { - "left": 76.82113233435703, - "top": 668.9008028213834 + "left": 77.546875, + "top": 667.4062589014521 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", + "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, - "type": "data_collection_input", - "uuid": "020f7580-f647-471f-b210-dbf9dfcf80bf", + "type": "parameter_input", + "uuid": "7aae38b8-39a8-4fba-bc6b-bda8c1ea9162", "when": null, "workflow_outputs": [] }, @@ -187,15 +175,15 @@ "inputs": [ { "description": "Whether to report QC", - "name": "Generate QC reports?" + "name": "Generate QC reports" } ], - "label": "Generate QC reports?", + "label": "Generate QC reports", "name": "Input parameter", "outputs": [], "position": { - "left": 117.49850394573046, - "top": 779.5931018245802 + "left": 114.671875, + "top": 764.5781339014521 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -203,13 +191,7 @@ "type": "parameter_input", "uuid": "bea331ce-d6fa-4312-8dce-a8b13bc4e77b", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "a3d78ed2-e961-4d34-9a7e-68a6872c64ac" - } - ] + "workflow_outputs": [] }, "4": { "annotation": "Select the reference genome", @@ -227,8 +209,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 147.49847445771462, - "top": 891.2288050461835 + "left": 157.109375, + "top": 870.218728383874 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -236,13 +218,7 @@ "type": "parameter_input", "uuid": "a72b29ae-65a7-4e4d-a996-2943ab5b02aa", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "b6a5f44e-06f4-4ac9-811b-40a2b48252c6" - } - ] + "workflow_outputs": [] }, "5": { "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", @@ -260,8 +236,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 197.4984987055553, - "top": 988.4006367761568 + "left": 199.671875, + "top": 977.3906033838739 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -272,70 +248,58 @@ "workflow_outputs": [] }, "6": { - "annotation": "Use featureCounts tool instead of RNA STAR?", + "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", "content_id": null, "errors": null, "id": 6, "input_connections": {}, "inputs": [ { - "description": "Use featureCounts tool instead of RNA STAR?", - "name": "Use featureCounts for generating count tables" + "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "name": "Strandedness" } ], - "label": "Use featureCounts for generating count tables", + "label": "Strandedness", "name": "Input parameter", "outputs": [], "position": { - "left": 237.15865423690892, - "top": 1097.1340383001116 + "left": 251.890625, + "top": 1073.781228383874 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", + "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", + "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "f8a0a43f-d4b3-42ad-a565-82974ebc035f" - } - ] + "workflow_outputs": [] }, "7": { - "annotation": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", + "annotation": "Use featureCounts tool instead of RNA STAR?", "content_id": null, "errors": null, "id": 7, "input_connections": {}, "inputs": [ { - "description": "For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence", - "name": "strandedness" + "description": "Use featureCounts tool instead of RNA STAR?", + "name": "Use featureCounts for generating count tables" } ], - "label": "strandedness", + "label": "Use featureCounts for generating count tables", "name": "Input parameter", "outputs": [], "position": { - "left": 280.70402093882234, - "top": 1232.7860110851007 + "left": 291.34375, + "top": 1173.124978383874 }, "tool_id": null, - "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "2ccf2242-dddd-45b6-8cea-746d9b5d49bc", + "uuid": "f43d45e6-5692-41cb-8cfc-205dbeab1bd0", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "0f6c75c7-6c9b-4a75-ae8a-450ee390a843" - } - ] + "workflow_outputs": [] }, "8": { "annotation": "Whether FPKM values should be computed with Cufflinks", @@ -346,15 +310,15 @@ "inputs": [ { "description": "Whether FPKM values should be computed with Cufflinks", - "name": "Compute Cufflinks FPKM?" + "name": "Compute Cufflinks FPKM" } ], - "label": "Compute Cufflinks FPKM?", + "label": "Compute Cufflinks FPKM", "name": "Input parameter", "outputs": [], "position": { - "left": 305.59290083057465, - "top": 1327.9254709507823 + "left": 346.83340121591186, + "top": 1309.3879390873915 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -362,13 +326,7 @@ "type": "parameter_input", "uuid": "78868cdb-baff-4388-a41a-a700259da1ed", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "38a0fd86-4369-4f85-9f42-911b6e478b4a" - } - ] + "workflow_outputs": [] }, "9": { "annotation": "It could be a GTF with for example one entry for the chrM forward and one entry for the chrM reverse", @@ -386,8 +344,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 336.93486951390355, - "top": 1446.2136308123108 + "left": 380.53912206977975, + "top": 1425.307227138327 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -395,13 +353,7 @@ "type": "data_input", "uuid": "0d4e1623-adc9-4ff3-8156-7e1322b1e278", "when": null, - "workflow_outputs": [ - { - "label": null, - "output_name": "output", - "uuid": "b9385caf-799d-4e0e-a1e6-97868d2233ea" - } - ] + "workflow_outputs": [] }, "10": { "annotation": "Whether FPKM values should be computed with StringTie", @@ -412,15 +364,15 @@ "inputs": [ { "description": "Whether FPKM values should be computed with StringTie", - "name": "Compute StringTie FPKM?" + "name": "Compute StringTie FPKM" } ], - "label": "Compute StringTie FPKM?", + "label": "Compute StringTie FPKM", "name": "Input parameter", "outputs": [], "position": { - "left": 345.60201891969245, - "top": 1567.401056132716 + "left": 406.9259176995931, + "top": 1559.4856968335116 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", @@ -428,30 +380,57 @@ "type": "parameter_input", "uuid": "056f11f4-bdd9-4361-b037-2c0822320cc2", "when": null, - "workflow_outputs": [ + "workflow_outputs": [] + }, + "11": { + "annotation": "", + "content_id": "__FLATTEN__", + "errors": null, + "id": 11, + "input_connections": { + "input": { + "id": 0, + "output_name": "output" + } + }, + "inputs": [], + "label": null, + "name": "Flatten collection", + "outputs": [ { - "label": null, - "output_name": "output", - "uuid": "8dd69bcb-492c-4566-9cd7-50caaa30aa7f" + "name": "output", + "type": "input" } - ] + ], + "position": { + "left": 430.77112544776327, + "top": 623.8873433527641 + }, + "post_job_actions": {}, + "tool_id": "__FLATTEN__", + "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"join_identifier\": \"_\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.0.0", + "type": "tool", + "uuid": "dddbd652-fe4f-42c8-a2ff-bdc259d4928c", + "when": null, + "workflow_outputs": [] }, - "11": { + "12": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1", "errors": null, - "id": 11, + "id": 12, "input_connections": { "library|input_1": { - "id": 2, + "id": 0, "output_name": "output" }, "library|r1|adapters_0|adapter_source|adapter": { - "id": 0, + "id": 1, "output_name": "output" }, "library|r2|adapters2_0|adapter_source|adapter": { - "id": 1, + "id": 2, "output_name": "output" } }, @@ -474,8 +453,8 @@ } ], "position": { - "left": 374.33462420145804, - "top": 269.76267157128495 + "left": 382.52212406111795, + "top": 267.76267157128495 }, "post_job_actions": { "HideDatasetActionout1": { @@ -508,39 +487,6 @@ "when": null, "workflow_outputs": [] }, - "12": { - "annotation": "", - "content_id": "__FLATTEN__", - "errors": null, - "id": 12, - "input_connections": { - "input": { - "id": 2, - "output_name": "output" - } - }, - "inputs": [], - "label": null, - "name": "Flatten collection", - "outputs": [ - { - "name": "output", - "type": "input" - } - ], - "position": { - "left": 422.58362558810336, - "top": 625.8873433527641 - }, - "post_job_actions": {}, - "tool_id": "__FLATTEN__", - "tool_state": "{\"input\": {\"__class__\": \"ConnectedValue\"}, \"join_identifier\": \"_\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.0.0", - "type": "tool", - "uuid": "dddbd652-fe4f-42c8-a2ff-bdc259d4928c", - "when": null, - "workflow_outputs": [] - }, "13": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1", @@ -562,8 +508,8 @@ } ], "position": { - "left": 1489.6076401751156, - "top": 1175.104961480357 + "left": 1497.7951400347756, + "top": 1173.104961480357 }, "post_job_actions": { "HideDatasetActionout1": { @@ -593,7 +539,7 @@ "id": 14, "input_connections": { "input_param_type|input_param": { - "id": 7, + "id": 6, "output_name": "output" } }, @@ -612,8 +558,8 @@ } ], "position": { - "left": 871.929384855411, - "top": 1305.1637555172579 + "left": 880.1168847150709, + "top": 1303.1637555172579 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -643,7 +589,7 @@ "id": 15, "input_connections": { "input_param_type|input_param": { - "id": 7, + "id": 6, "output_name": "output" } }, @@ -662,8 +608,8 @@ } ], "position": { - "left": 872.1470350742542, - "top": 1485.3515528952898 + "left": 880.334534933914, + "top": 1483.3515528952898 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -693,7 +639,7 @@ "id": 16, "input_connections": { "input_param_type|input_param": { - "id": 7, + "id": 6, "output_name": "output" } }, @@ -712,8 +658,8 @@ } ], "position": { - "left": 867.4070007672439, - "top": 1655.5777444451405 + "left": 875.5945006269037, + "top": 1653.5777444451405 }, "post_job_actions": { "HideDatasetActionoutput_param_text": { @@ -751,7 +697,7 @@ "output_name": "output" }, "singlePaired|input": { - "id": 11, + "id": 12, "output_name": "out_pairs" } }, @@ -798,8 +744,8 @@ } ], "position": { - "left": 723.9734479297246, - "top": 248.8799136582777 + "left": 732.1609477893844, + "top": 246.8799136582777 }, "post_job_actions": { "HideDatasetActionsignal_unique_str1": { @@ -887,8 +833,8 @@ "name": "Get Uniquely mapped unstranded coverage", "outputs": [], "position": { - "left": 1700.9200092091487, - "top": 86.70585901249711 + "left": 1683.2031849964808, + "top": 86.70584740647254 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1236,7 +1182,7 @@ "output_name": "signal_unique_str2" }, "strandedness": { - "id": 7, + "id": 6, "input_subworkflow_step_id": 0, "output_name": "output" } @@ -1251,8 +1197,8 @@ "name": "Re-arrange Stranded RNA-seq coverage", "outputs": [], "position": { - "left": 1709.927313955971, - "top": 282.0471666714667 + "left": 1692.210489743303, + "top": 282.0471550654421 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1801,11 +1747,6 @@ "uuid": "bf990b24-1ec8-4e67-acec-fecf26a3d49f", "when": null, "workflow_outputs": [ - { - "label": null, - "output_name": "0:output", - "uuid": "29b82c83-0c21-4052-94ee-343267c81ce9" - }, { "label": "Stranded Coverage", "output_name": "Uniquely Mapped Stranded Coverage", @@ -1832,7 +1773,7 @@ "output_name": "output_param_text" }, "when": { - "id": 6, + "id": 7, "output_name": "output" } }, @@ -1855,8 +1796,8 @@ } ], "position": { - "left": 1705.725695820465, - "top": 674.9994811085061 + "left": 1713.913195680125, + "top": 672.9994811085061 }, "post_job_actions": {}, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2", @@ -1919,8 +1860,8 @@ } ], "position": { - "left": 1723.5484887804166, - "top": 1426.2142641508385 + "left": 1731.7359886400766, + "top": 1424.2142641508385 }, "post_job_actions": { "HideDatasetActionoutput_gtf": { @@ -2026,8 +1967,8 @@ } ], "position": { - "left": 1990.0937720526786, - "top": 1152.343757982693 + "left": 1998.2812719123385, + "top": 1150.343757982693 }, "post_job_actions": { "HideDatasetActionassembled_isoforms": { @@ -2073,15 +2014,15 @@ "uuid": "af5419b7-ae6b-498c-8123-f609b8fcd8b4", "when": "$(inputs.when)", "workflow_outputs": [ - { - "label": "Genes Expression from Cufflinks", - "output_name": "genes_expression", - "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" - }, { "label": "Transcripts Expression from Cufflinks", "output_name": "transcripts_expression", "uuid": "2c13ef79-948c-4f5f-8516-a769550128fd" + }, + { + "label": "Genes Expression from Cufflinks", + "output_name": "genes_expression", + "uuid": "3bd4fbda-f241-4ebd-b7a5-dea7271c521e" } ] }, @@ -2095,7 +2036,7 @@ "output_name": "reads_per_gene" }, "Strandness param": { - "id": 7, + "id": 6, "input_subworkflow_step_id": 2, "output_name": "output" }, @@ -2115,8 +2056,8 @@ "name": "Process Count files", "outputs": [], "position": { - "left": 2152.918395886789, - "top": 667.1799212422835 + "left": 2161.105895746449, + "top": 665.1799212422835 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -2569,11 +2510,6 @@ "label": "FeatureCounts Summary Table", "output_name": "FeatureCounts Summary Table", "uuid": "6bebc1fb-139b-4aba-82c2-4f53476f59af" - }, - { - "label": null, - "output_name": "2:output", - "uuid": "1e5792e4-08cd-4f03-9fb7-5276b3680a21" } ] }, @@ -2582,12 +2518,12 @@ "id": 24, "input_connections": { "Cutadapt Reports": { - "id": 11, + "id": 12, "input_subworkflow_step_id": 2, "output_name": "report" }, "FASTQ collection": { - "id": 12, + "id": 11, "input_subworkflow_step_id": 0, "output_name": "output" }, @@ -2626,8 +2562,8 @@ "name": "RNA-seq-Paired-QC", "outputs": [], "position": { - "left": 2527.234117718266, - "top": 628.3664416590253 + "left": 2465.503860179348, + "top": 451.63585583919314 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -3240,8 +3176,9 @@ } }, "tags": [ - "RNAseq" + "RNAseq", + "transcriptomics" ], - "uuid": "e21c4a06-b5ec-4691-8511-c5ffb12ac8f4", - "version": 16 -} \ No newline at end of file + "uuid": "3eb40117-2053-4cab-ba1d-d4e31d8b997f", + "version": 20 +} From 8930c62d5952576b00253f751038f6f4b97748b4 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Sat, 26 Oct 2024 11:17:47 +0200 Subject: [PATCH 38/47] correct the workflow name in -tests.yml --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 12b0702ae..cb197bc23 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -1,4 +1,4 @@ -- doc: Test outline for rnaseq-pe +- doc: Test outline for RNAseq_PE job: GTF file of annotation: class: File From 94aaca98de96049546d107ae345f8bae8f5e5f76 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 30 Oct 2024 07:51:38 +0100 Subject: [PATCH 39/47] correct the Zenodo record in the CHANGELOG --- workflows/transcriptomics/rnaseq-pe/CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 95251a078..15fbc6ad2 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -3,7 +3,7 @@ ## [0.10] 2024-09-23 ### Manual update -- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/4541751 +- Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631 - Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, featureCounts and Picard reports - Added featureCounts as an alternative way to generate count files From 13dc7185958732d5a51c9fa527dc03e0926432b2 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 08:09:10 +0100 Subject: [PATCH 40/47] fix tests --- .../rnaseq-pe/rnaseq-pe-tests.yml | 28 +++++++++++-------- 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index cb197bc23..c50bf5681 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -37,13 +37,15 @@ Stranded Coverage: element_tests: SRR5085167_forward: - has_size: - value: 635210 - delta: 30000 + asserts: + has_size: + value: 635210 + delta: 30000 SRR5085167_reverse: - has_size: - value: 618578 - delta: 30000 + asserts: + has_size: + value: 618578 + delta: 30000 Gene Abundance Estimates from StringTie: element_tests: SRR5085167: @@ -53,15 +55,17 @@ Unstranded Coverage: element_tests: SRR5085167: - has_size: - value: 1140004 - delta: 50000 + asserts: + has_size: + value: 1140004 + delta: 50000 Mapped Reads: element_tests: SRR5085167: - has_size: - value: 56913572 - delta: 2500000 + asserts: + has_size: + value: 56913572 + delta: 2500000 Genes Expression from Cufflinks: element_tests: SRR5085167: From 2c0ab7547e7c4c3acc2c38b781de92a3dddb159b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 08:13:21 +0100 Subject: [PATCH 41/47] update workflow to: - use fastp instead of cutadapt which allows optional adapters - generate a combined report if additional QC are not wanted - include the gene counts from STAR in the multiQC - hide more intermediate outputs - do not consider FeatureCounts Summary Table as a workflow output --- .../rnaseq-pe/rnaseq-pe-tests.yml | 10 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 648 ++++++++++++------ 2 files changed, 441 insertions(+), 217 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index c50bf5681..74f771bcf 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -20,7 +20,7 @@ location: https://zenodo.org/records/13987631/files/SRR5085167_reverse.fastqsanger.gz Forward adapter: AGATCGGAAGAG Reverse adapter: GATCGTCGGACT - Generate QC reports: true + Generate additional QC reports: true Reference genome: sacCer3 Use featureCounts for generating count tables: true Strandedness: stranded - forward @@ -83,10 +83,4 @@ SRR5085167: asserts: has_line: - line: "YAL038W 1609" - FeatureCounts Summary Table: - element_tests: - SRR5085167: - asserts: - has_line: - line: "Assigned 101987" \ No newline at end of file + line: "YAL038W 1609" \ No newline at end of file diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 0d3b09c6b..888ebedd3 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,12 +1,12 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. Alternatively, featureCounts can be used to count the reads/fragments per gene. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.\n", + "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with fastp. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. Alternatively, featureCounts can be used to count the reads/fragments per gene. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.\n", "comments": [ { "child_steps": [ - 13, - 21, - 22 + 14, + 22, + 23 ], "color": "yellow", "data": { @@ -25,9 +25,9 @@ }, { "child_steps": [ - 14, 15, - 16 + 16, + 17 ], "color": "lime", "data": { @@ -46,8 +46,8 @@ }, { "child_steps": [ - 18, - 19 + 19, + 20 ], "color": "red", "data": { @@ -80,7 +80,7 @@ "format-version": "0.1", "license": "MIT", "release": "0.10", - "name": "RNAseq_PE", + "name": "RNA-seq for Paired-end fastqs", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -101,7 +101,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 462.87500890145213 }, "tool_id": null, @@ -113,14 +113,14 @@ "workflow_outputs": [] }, "1": { - "annotation": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "annotation": "This is optional. Fastp will use overlapping. If you want to specify, for Nextera use: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, for TruSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "content_id": null, "errors": null, "id": 1, "input_connections": {}, "inputs": [ { - "description": "Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", + "description": "This is optional. Fastp will use overlapping. If you want to specify, for Nextera use: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC, for TruSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC", "name": "Forward adapter" } ], @@ -132,7 +132,7 @@ "top": 567.328103383874 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "6d1de206-97c4-41ba-8702-a980f748a689", @@ -140,14 +140,14 @@ "workflow_outputs": [] }, "2": { - "annotation": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "annotation": "This is optional. Fastp will use overlapping. If you want to specify, for Nextera use: CTGTCTCTTATACACATCTGACGCTGCCGACGA, for TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", "content_id": null, "errors": null, "id": 2, "input_connections": {}, "inputs": [ { - "description": "Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", + "description": "This is optional. Fastp will use overlapping. If you want to specify, for Nextera use: CTGTCTCTTATACACATCTGACGCTGCCGACGA, for TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT", "name": "Reverse adapter" } ], @@ -159,7 +159,7 @@ "top": 667.4062589014521 }, "tool_id": null, - "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"text\", \"optional\": true}", "tool_version": null, "type": "parameter_input", "uuid": "7aae38b8-39a8-4fba-bc6b-bda8c1ea9162", @@ -167,18 +167,18 @@ "workflow_outputs": [] }, "3": { - "annotation": "Whether to report QC", + "annotation": "Whether to compute additional QC like fastQC, gene body coverage etc...", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "Whether to report QC", - "name": "Generate QC reports" + "description": "Whether to compute additional QC like fastQC, gene body coverage etc...", + "name": "Generate additional QC reports" } ], - "label": "Generate QC reports", + "label": "Generate additional QC reports", "name": "Input parameter", "outputs": [], "position": { @@ -406,7 +406,13 @@ "left": 430.77112544776327, "top": 623.8873433527641 }, - 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"uuid": "8518a66b-6e91-4252-a543-0109bf7bb75e" + "uuid": "7a36b35e-4487-49d8-b6e1-45a2063a5fff" }, "tool_id": null, "type": "subworkflow", @@ -3179,6 +3409,6 @@ "RNAseq", "transcriptomics" ], - "uuid": "3eb40117-2053-4cab-ba1d-d4e31d8b997f", - "version": 20 -} + "uuid": "541ebcef-a7ea-42de-8597-97a18555eaab", + "version": 6 +} \ No newline at end of file From 720313dfefc5be78d979413abddeef5dd75b2164 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 08:38:18 +0100 Subject: [PATCH 42/47] update README CHANGELOG and version --- workflows/transcriptomics/rnaseq-pe/CHANGELOG.md | 11 +++++++---- workflows/transcriptomics/rnaseq-pe/README.md | 7 ++++--- workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga | 2 +- 3 files changed, 12 insertions(+), 8 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 15fbc6ad2..02c637982 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -1,11 +1,14 @@ # Changelog -## [0.10] 2024-09-23 +## [1.0] 2024-09-23 -### Manual update +### Changes in workflows +- Add an optional subworkflow with more QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes. +- Add featureCounts as an alternative way to generate count files +- Use fastp instead of cutadapt which uses pair overlap and allows to have optional adapter sequences + +### Test dataset - Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631 -- Added a subworkflow with MultiQC on FastQC, Cutadapt, STAR, featureCounts and Picard reports -- Added featureCounts as an alternative way to generate count files ## [0.9] 2024-09-23 diff --git a/workflows/transcriptomics/rnaseq-pe/README.md b/workflows/transcriptomics/rnaseq-pe/README.md index 93489bf62..4ba99e13c 100644 --- a/workflows/transcriptomics/rnaseq-pe/README.md +++ b/workflows/transcriptomics/rnaseq-pe/README.md @@ -15,8 +15,8 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM ## Inputs values -- Forward and Reverse adapter: this depends on the library preparation. Usually classical Illumina RNA libraries are Truseq and ISML (relatively new Illumina library) is Nextera. If you don't know, use FastQC to determine if it is Truseq or Nextera. If the read length is relatively short (50bp), there is probably no adapter so it will not impact your results. -- Generate QC reports: whether to generate an aggrigated MultiQC report from FastQC, Cutadapt, STAR, featureCounts and Picard. +- Forward and Reverse adapter (optional): By default, fastp will try to overlap both reads and will only use these sequences if R1/R2 are found not overlapped. Their sequences depends on the library preparation. Usually classical Illumina RNA libraries is Truseq and ISML (relatively new Illumina library) is Nextera. +- Generate additional QC reports: whether to compute additional QC: FastQC, Picard, Read distribution on genomic features, gene body coverage, reads per chromosomes. - Reference genome: this field will be adapted to the genomes available for STAR. - Strandedness: For stranded RNA, reverse means that the first read in a pair is complementary to the coding sequence, forward means that the first read in a pair is in the same orientation as the coding sequence. This will only count alignments that are compatible with your library preparation strategy. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. - Use featureCounts for generating count tables: Whether to use count tables from featureCounts instead of from STAR. @@ -28,9 +28,10 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM - The workflow will remove adapters and low quality bases and filter out any read smaller than 15bp. - The filtered reads are mapped with STAR with ENCODE parameters (for long RNA-seq but I use it for short also). STAR is also used to count reads per gene and generate strand-specific normalized coverage (on uniquely mapped reads). - Optionally featureCounts is used to generate count files when this option enabled. +- Optionally FastQC, Picard, read_distribution, geneBody_coverage, samtools idxstats, Picard are run to get additional QC. - A multiQC is run to have an overview of the QC. This can also be used to get the strandedness. - FPKM values for genes and transcripts are computed with cufflinks using correction for multi-mapped reads (this step is optionnal). -- FPKM/TPM values for genes are computed with StringTie. +- FPKM/TPM values for genes are computed with StringTie (this step is optional). - The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1). - Unstranded coverage is computed with bedtools and normalized to the number of million uniquely mapped reads. - The three coverage files are converted to bigwig. diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 888ebedd3..625d54098 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -79,7 +79,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.10", + "release": "1.0", "name": "RNA-seq for Paired-end fastqs", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" From b2e87146c826008126c35f9650bd4107c872ec49 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 10:03:48 +0100 Subject: [PATCH 43/47] update cufflinks --- .../transcriptomics/rnaseq-pe/CHANGELOG.md | 3 + .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 62 ++++++++++--------- 2 files changed, 36 insertions(+), 29 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 02c637982..14ece7a3f 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -7,6 +7,9 @@ - Add featureCounts as an alternative way to generate count files - Use fastp instead of cutadapt which uses pair overlap and allows to have optional adapter sequences +### Tool update +- `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4` + ### Test dataset - Using a new subsampled Yeast test data from Zenodo record https://zenodo.org/records/13987631 diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 625d54098..dc0752fca 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -2,27 +2,6 @@ "a_galaxy_workflow": "true", "annotation": "This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with fastp. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously as well as normalized coverage (per million mapped reads) on uniquely mapped reads. The counts are reprocessed to be similar to HTSeq-count output. Alternatively, featureCounts can be used to count the reads/fragments per gene. FPKM are computed with cufflinks and/or with StringTie. The unstranded normalized coverage is computed with bedtools.\n", "comments": [ - { - "child_steps": [ - 14, - 22, - 23 - ], - "color": "yellow", - "data": { - "title": "Additional quantification" - }, - "id": 2, - "position": [ - 1391.2086321940171, - 1073.6999999999998 - ], - "size": [ - 860, - 716 - ], - "type": "frame" - }, { "child_steps": [ 15, @@ -63,6 +42,27 @@ 538 ], "type": "frame" + }, + { + "child_steps": [ + 14, + 22, + 23 + ], + "color": "yellow", + "data": { + "title": "Additional quantification" + }, + "id": 2, + "position": [ + 1391.2086321940171, + 1073.6999999999998 + ], + "size": [ + 860, + 716 + ], + "type": "frame" } ], "creator": [ @@ -1971,7 +1971,7 @@ }, "23": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4", "errors": null, "id": 23, "input_connections": { @@ -2009,6 +2009,10 @@ "description": "runtime parameter for tool Cufflinks", "name": "advanced_settings" }, + { + "description": "runtime parameter for tool Cufflinks", + "name": "input" + }, { "description": "runtime parameter for tool Cufflinks", "name": "reference_annotation" @@ -2073,15 +2077,15 @@ "output_name": "transcripts_expression" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.4", "tool_shed_repository": { - "changeset_revision": "d080005cffe1", + "changeset_revision": "6926716bbfb5", "name": "cufflinks", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"ConnectedValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"ConnectedValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"ConnectedValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.2.1.3", + "tool_state": "{\"advanced_settings\": {\"use_advanced_settings\": \"Yes\", \"__current_case__\": 1, \"library_type\": {\"__class__\": \"ConnectedValue\"}, \"mask_file\": {\"__class__\": \"RuntimeValue\"}, \"inner_mean_dist\": \"200\", \"inner_dist_std_dev\": \"80\", \"max_mle_iterations\": \"5000\", \"junc_alpha\": \"0.001\", \"small_anchor_fraction\": \"0.09\", \"overhang_tolerance\": \"8\", \"max_bundle_length\": \"10000000\", \"max_bundle_frags\": \"1000000\", \"min_intron_length\": \"50\", \"trim_three_avgcov_thresh\": \"10\", \"trim_three_dropoff_frac\": \"0.1\"}, \"bias_correction\": {\"do_bias_correction\": \"Yes\", \"__current_case__\": 0, \"seq_source\": {\"index_source\": \"cached\", \"__current_case__\": 0, \"index\": {\"__class__\": \"ConnectedValue\"}}}, \"global_model\": null, \"input\": {\"__class__\": \"RuntimeValue\"}, \"length_correction\": \"--no-effective-length-correction\", \"max_intron_len\": \"300000\", \"min_isoform_fraction\": \"0.1\", \"multiread_correct\": true, \"pre_mrna_fraction\": \"0.15\", \"reference_annotation\": {\"use_ref\": \"Use reference annotation\", \"__current_case__\": 1, \"reference_annotation_file\": {\"__class__\": \"RuntimeValue\"}, \"compatible_hits_norm\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.2.1.4", "type": "tool", "uuid": "af5419b7-ae6b-498c-8123-f609b8fcd8b4", "when": "$(inputs.when)", @@ -2632,7 +2636,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"RuntimeValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"RuntimeValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"RuntimeValue\"}}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"featureCounts\", \"__current_case__\": 9, \"input\": {\"__class__\": \"ConnectedValue\"}}}], \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "8ad489c5-92b6-4e73-99a4-543923bea427", @@ -3409,6 +3413,6 @@ "RNAseq", "transcriptomics" ], - "uuid": "541ebcef-a7ea-42de-8597-97a18555eaab", - "version": 6 + "uuid": "5ab1d724-01d4-4673-a3c3-ae2bc944458f", + "version": 1 } \ No newline at end of file From 085aa0ebbc787537e259c5c96c2d1d87871903ad Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 12:08:29 +0100 Subject: [PATCH 44/47] Change test results --- .../transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 74f771bcf..18e6d3d0c 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -32,8 +32,8 @@ asserts: has_text_matching: expression: "SRR5085167\t0.10[0-9]*\t16.16[0-9]*\t43.61[0-9]*\t0.33[0-9]*\t0.31[0-9]*\t93.43\t0.11[0-9]*\t34.13\t0.19[0-9]*\t44.15[0-9]*\t\t\t\t\t\t" - expression: "SRR5085167_forward\t\t\t\t\t\t\t\t\t\t\t36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" - expression: "SRR5085167_reverse\t\t\t\t\t\t\t\t\t\t\t35.31[0-9]*\t46.0\t75.0\t75\t45.45[0-9]*\t0.39[0-9]*" + expression: "SRR5085167_forward\t*36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" + expression: "SRR5085167_reverse\t*35.31[0-9]*\t46.0\t75.0\t75\t45.45[0-9]*\t0.39[0-9]*" Stranded Coverage: element_tests: SRR5085167_forward: @@ -51,7 +51,7 @@ SRR5085167: asserts: has_text_matching: - expression: "YAL038W\tCDC19\tchrI\t\\+\t71786\t73288\t91.35[0-9]*\t3187.55[0-9]*\t3870.16[0-9]*" + expression: "YAL038W\tCDC19\tchrI\t\\+\t71786\t73288\t92.5[0-9]*\t3273.9[0-9]*\t3900.[0-9]*" Unstranded Coverage: element_tests: SRR5085167: @@ -71,16 +71,16 @@ SRR5085167: asserts: has_line: - line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3376.27 3155.33 3597.21 OK" + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3437.1 3211.44 3662.76 OK" Transcripts Expression from Cufflinks: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 102.307 3376.27 3155.33 3597.21 OK" + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 102.837 3437.1 3211.44 3662.76 OK" Counts Table: element_tests: SRR5085167: asserts: has_line: - line: "YAL038W 1609" \ No newline at end of file + line: "YAL038W 1591" \ No newline at end of file From dcf48ddf6dd6360f2873b189467a9bf891b2c31d Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 12:09:53 +0100 Subject: [PATCH 45/47] Fix assertion with multiple expressions --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 18e6d3d0c..fe6e26aa3 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -30,9 +30,11 @@ outputs: MultiQC stats: asserts: - has_text_matching: + - that: "has_text_matching" expression: "SRR5085167\t0.10[0-9]*\t16.16[0-9]*\t43.61[0-9]*\t0.33[0-9]*\t0.31[0-9]*\t93.43\t0.11[0-9]*\t34.13\t0.19[0-9]*\t44.15[0-9]*\t\t\t\t\t\t" + - that: "has_text_matching" expression: "SRR5085167_forward\t*36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" + - that: "has_text_matching" expression: "SRR5085167_reverse\t*35.31[0-9]*\t46.0\t75.0\t75\t45.45[0-9]*\t0.39[0-9]*" Stranded Coverage: element_tests: From 98a95c5313f7ed023b490501eaab709c8f0c2c83 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 12:20:57 +0100 Subject: [PATCH 46/47] fix indentation of expression after that --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index fe6e26aa3..d52fa6f64 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -31,11 +31,11 @@ MultiQC stats: asserts: - that: "has_text_matching" - expression: "SRR5085167\t0.10[0-9]*\t16.16[0-9]*\t43.61[0-9]*\t0.33[0-9]*\t0.31[0-9]*\t93.43\t0.11[0-9]*\t34.13\t0.19[0-9]*\t44.15[0-9]*\t\t\t\t\t\t" + expression: "SRR5085167\t0.10[0-9]*\t16.16[0-9]*\t43.61[0-9]*\t0.33[0-9]*\t0.31[0-9]*\t93.43\t0.11[0-9]*\t34.13\t0.19[0-9]*\t44.15[0-9]*\t\t\t\t\t\t" - that: "has_text_matching" - expression: "SRR5085167_forward\t*36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" + expression: "SRR5085167_forward\t*36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" - that: "has_text_matching" - expression: "SRR5085167_reverse\t*35.31[0-9]*\t46.0\t75.0\t75\t45.45[0-9]*\t0.39[0-9]*" + expression: "SRR5085167_reverse\t*35.31[0-9]*\t46.0\t75.0\t75\t45.45[0-9]*\t0.39[0-9]*" Stranded Coverage: element_tests: SRR5085167_forward: From 93049d0f05f503ba50229de763943a2986555900 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 13 Nov 2024 12:49:12 +0100 Subject: [PATCH 47/47] update multiQC output in test --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index d52fa6f64..b78b90301 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -31,7 +31,7 @@ MultiQC stats: asserts: - that: "has_text_matching" - expression: "SRR5085167\t0.10[0-9]*\t16.16[0-9]*\t43.61[0-9]*\t0.33[0-9]*\t0.31[0-9]*\t93.43\t0.11[0-9]*\t34.13\t0.19[0-9]*\t44.15[0-9]*\t\t\t\t\t\t" + expression: "SRR5085167\t0.10[0-9]*\t16.45[0-9]*\t43.38[0-9]*\t0.32[0-9]*\t0.30[0-9]*\t93.75\t0.11[0-9]*\t34.29\t0.19[0-9]*\t17.6[0-9]*\t91.8[0-9]*\t30.0[0-9]*\t0.64[0-9]*\t43.5[0-9]*\t81.0[0-9]*\t72.6[0-9]*\t" - that: "has_text_matching" expression: "SRR5085167_forward\t*36.33[0-9]*\t46.0\t75.0\t75\t27.27[0-9]*\t0.39[0-9]*" - that: "has_text_matching"