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 64d12ef64..14ece7a3f 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -1,5 +1,18 @@ # Changelog +## [1.0] 2024-09-23 + +### 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 + +### 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 + ## [0.9] 2024-09-23 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-pe/README.md b/workflows/transcriptomics/rnaseq-pe/README.md index 3640d4976..4ba99e13c 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: @@ -15,19 +15,23 @@ 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 (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. +- 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. +- 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-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 76be417ce..b78b90301 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -1,99 +1,88 @@ - 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/13987631/files/Saccharomyces_cerevisiae.R64-1-1.113.gtf filetype: gtf - PE fastq input: + Collection paired FASTQ files: class: Collection collection_type: list:paired elements: - class: Collection type: paired - identifier: GSM461177 + identifier: SRR5085167 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 - strandedness: unstranded - cufflinks_FPKM: false - stringtie_FPKM: true + - class: File + identifier: forward + location: https://zenodo.org/records/13987631/files/SRR5085167_forward.fastqsanger.gz + - class: File + identifier: reverse + location: https://zenodo.org/records/13987631/files/SRR5085167_reverse.fastqsanger.gz + Forward adapter: AGATCGGAAGAG + Reverse adapter: GATCGTCGGACT + Generate additional QC reports: true + 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 outputs: - output_log: + MultiQC stats: + asserts: + - that: "has_text_matching" + 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" + 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: - GSM461177: + SRR5085167_forward: 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: 635210 + delta: 30000 + SRR5085167_reverse: 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: 618578 + delta: 30000 + Gene Abundance Estimates from StringTie: element_tests: - GSM461177: + SRR5085167: asserts: - - that: "has_text" - text: "N_ambiguous 25107 5900 5518" - - that: "has_text" - text: "FBgn0010247 13 5 8" - HTS count like output: + has_text_matching: + expression: "YAL038W\tCDC19\tchrI\t\\+\t71786\t73288\t92.5[0-9]*\t3273.9[0-9]*\t3900.[0-9]*" + Unstranded Coverage: element_tests: - GSM461177: + SRR5085167: asserts: - has_text: - text: "FBgn0010247\t13" - both strands coverage: + has_size: + value: 1140004 + delta: 50000 + Mapped Reads: element_tests: - GSM461177: + SRR5085167: asserts: has_size: - value: 9885639 - delta: 900000 - stranded coverage: + value: 56913572 + delta: 2500000 + Genes Expression from Cufflinks: element_tests: - GSM461177_reverse: + SRR5085167: asserts: - has_size: - value: 5920766 - delta: 600000 - GSM461177_forward: + has_line: + line: "YAL038W - - YAL038W CDC19 - chrI:71785-73288 - - 3437.1 3211.44 3662.76 OK" + Transcripts Expression from Cufflinks: + element_tests: + SRR5085167: asserts: - has_size: - value: 5920766 - delta: 600000 - genes_expression_stringtie: + has_line: + line: "YAL038W_mRNA - - YAL038W CDC19 - chrI:71785-73288 1503 102.837 3437.1 3211.44 3662.76 OK" + Counts Table: element_tests: - GSM461177: + SRR5085167: asserts: - has_text: - text: "FBgn0031217\tCG11377\tchr2L\t+\t102380\t104142\t1.963814\t33.024075\t62.009155" + has_line: + line: "YAL038W 1591" \ 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 ca98e047a..dc0752fca 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,18 +1,89 @@ { "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.", - "comments": [], + "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": [ + 15, + 16, + 17 + ], + "color": "lime", + "data": { + "title": "Map Strandedness parameter" + }, + "id": 0, + "position": [ + 855.5086321940169, + 1252.5 + ], + "size": [ + 251, + 558 + ], + "type": "frame" + }, + { + "child_steps": [ + 19, + 20 + ], + "color": "red", + "data": { + "title": "Coverage Files" + }, + "id": 1, + "position": [ + 1603.68749985966, + 0 + ], + "size": [ + 375, + 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": [ { "class": "Person", - "identifier": "0000-0002-1964-4960", + "identifier": "https://orcid.org/0000-0002-1964-4960", "name": "Lucille Delisle" + }, + { + "class": "Person", + "identifier": "https://orcid.org/0000-0002-5192-126X", + "name": "Pavankumar Videm" } ], "format-version": "0.1", "license": "MIT", - "release": "0.9", - "name": "RNAseq_PE", + "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" + }, "steps": { "0": { "annotation": "Should be a list of paired-end RNA-seq fastqs", @@ -23,320 +94,458 @@ "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": 462.87500890145213 }, "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": "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", - "name": "forward_adapter" + "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" } ], - "label": "forward_adapter", + "label": "Forward adapter", "name": "Input parameter", "outputs": [], "position": { - "left": 26.45001220703125, - "top": 338.9083312721534 + "left": 35.17186494140515, + "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": "db025004-00b9-4fa0-b4ae-e47d58a615ae", + "uuid": "6d1de206-97c4-41ba-8702-a980f748a689", "when": null, "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", - "name": "reverse_adapter" + "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" } ], - "label": "reverse_adapter", + "label": "Reverse adapter", "name": "Input parameter", "outputs": [], "position": { - "left": 68, - "top": 427.04166257098154 + "left": 77.546875, + "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": "ad4f5c84-4a83-4d66-afe1-a7fdfc37f638", + "uuid": "7aae38b8-39a8-4fba-bc6b-bda8c1ea9162", "when": null, "workflow_outputs": [] }, "3": { - "annotation": "reference_genome", + "annotation": "Whether to compute additional QC like fastQC, gene body coverage etc...", "content_id": null, "errors": null, "id": 3, "input_connections": {}, "inputs": [ { - "description": "reference_genome", - "name": "reference_genome" + "description": "Whether to compute additional QC like fastQC, gene body coverage etc...", + "name": "Generate additional QC reports" } ], - "label": "reference_genome", + "label": "Generate additional QC reports", "name": "Input parameter", "outputs": [], "position": { - "left": 132.63336181640625, - "top": 522.134886401586 + "left": 114.671875, + "top": 764.5781339014521 }, "tool_id": null, - "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - "uuid": "9e037207-3243-489c-bc93-3eb388f5d962", + "uuid": "bea331ce-d6fa-4312-8dce-a8b13bc4e77b", "when": null, "workflow_outputs": [] }, "4": { - "annotation": "gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming", + "annotation": "Select the reference genome", "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": "Select the reference genome", + "name": "Reference genome" + } + ], + "label": "Reference genome", + "name": "Input parameter", + "outputs": [], + "position": { + "left": 157.109375, + "top": 870.218728383874 + }, + "tool_id": null, + "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", + "tool_version": null, + "type": "parameter_input", + "uuid": "a72b29ae-65a7-4e4d-a996-2943ab5b02aa", + "when": null, + "workflow_outputs": [] + }, + "5": { + "annotation": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", + "content_id": null, + "errors": null, + "id": 5, + "input_connections": {}, + "inputs": [ + { + "description": "GTF compatible with the reference genome. Mind the UCSC/Ensembl differences in chromosome naming.", + "name": "GTF file of annotation" } ], - "label": "gtf", + "label": "GTF file of annotation", "name": "Input dataset", "outputs": [], "position": { - "left": 150.60003662109375, - "top": 606.751585620336 + "left": 199.671875, + "top": 977.3906033838739 }, "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": [] }, - "5": { + "6": { "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": 6, "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", - 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"tool_version": "9.3+galaxy1", + "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": "77cf2304-36bf-4337-bc2d-bc4d8b831668", + "uuid": "59db7088-85bf-42ba-9dcd-76836f9d6310", "when": null, "workflow_outputs": [] }, @@ -916,7 +1075,7 @@ "id": 4, "input_connections": { "input1": { - "id": 3, + "id": 2, "output_name": "outfile" } }, @@ -930,8 +1089,8 @@ } ], "position": { - "left": 584.4666748046875, - "top": 327 + "left": 560, + "top": 0 }, "post_job_actions": { "HideDatasetActionfloat_param": { @@ -955,7 +1114,7 @@ "id": 5, "input_connections": { "input_type|input": { - "id": 2, + "id": 3, "output_name": "out_file1" }, "report|scale": { @@ -982,8 +1141,8 @@ } ], "position": { - "left": 855.418361599966, - "top": 226.99244090393722 + "left": 840, + "top": 12 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1027,13 +1186,13 @@ } ], "position": { - "left": 1104.4183615999664, - "top": 298.7166748046875 + "left": 1120, + "top": 67 }, "post_job_actions": { "RenameDatasetActionout_file1": { "action_arguments": { - "newname": "both strands coverage" + "newname": "Both Strands Coverage" }, "action_type": "RenameDatasetAction", "output_name": "out_file1" @@ -1047,55 +1206,60 @@ "when": null, "workflow_outputs": [ { - "label": "both strands coverage", + "label": "Both Strands Coverage", "output_name": "out_file1", - "uuid": "81faf6f8-1ec1-45f1-9e04-d2fd12a1ddc0" + "uuid": "73763ad9-c132-4764-ada6-eece0c30e74f" } ] } }, "tags": [], - "uuid": "fdfcabc8-5014-4574-85ab-0182cb11750f" + "uuid": "451bba09-1c21-4978-b693-4e64402c5787" }, "tool_id": null, "type": "subworkflow", - "uuid": "c46207a6-d625-4646-a72b-79dc2065044f", + "uuid": "6ce6314b-d339-40bf-9f0e-53ca525204be", "when": null, "workflow_outputs": [ { - "label": "both strands coverage", - "output_name": "both strands coverage", - "uuid": "9f2bf997-14f8-4307-90b4-dc068b02dcd6" + "label": "Unstranded Coverage", + "output_name": "Both Strands Coverage", + "uuid": "f90cc885-438b-49ee-b1d1-8ed45f7dea5c" } ] }, - "17": { + "20": { "annotation": "", - "id": 17, + "id": 20, "input_connections": { "Bedgraph strand 1": { - "id": 14, + "id": 18, "input_subworkflow_step_id": 1, "output_name": "signal_unique_str1" }, "Bedgraph strand 2": { - "id": 14, + "id": 18, "input_subworkflow_step_id": 2, "output_name": "signal_unique_str2" }, "strandedness": { - "id": 5, + "id": 6, "input_subworkflow_step_id": 0, "output_name": "output" } }, - "inputs": [], - "label": null, + "inputs": [ + { + "description": "", + "name": "Generate Stranded Coverage" + } + ], + "label": "Generate Stranded Coverage", "name": "Re-arrange Stranded RNA-seq coverage", "outputs": [], "position": { - "left": 1169, - "top": 591 + "left": 1692.210489743303, + "top": 282.0471550654421 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -1111,6 +1275,9 @@ "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", @@ -1129,7 +1296,7 @@ "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}", @@ -1141,19 +1308,19 @@ { "label": null, "output_name": "output", - "uuid": "2d815f2b-a706-43a8-a317-7dc434c6fea8" + "uuid": "d363c181-7f37-45ef-9732-86aaf879478a" } ] }, "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" } ], @@ -1161,8 +1328,8 @@ "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\"}", @@ -1188,8 +1355,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - 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"uuid": "4eb0d67c-f53c-4f84-90fc-3db41e4f0aa7", + "uuid": "ec10a98b-adb9-4037-9137-1717068d7157", "when": null, "workflow_outputs": [] }, @@ -1413,7 +1580,7 @@ } }, "inputs": [], - "label": "New labels strand 2", + "label": "New labels strand 1", "name": "Replace", "outputs": [ { @@ -1422,8 +1589,8 @@ } ], "position": { - "left": 821, - "top": 276 + "left": 569.999952609169, + "top": 328 }, "post_job_actions": { "HideDatasetActionoutfile": { @@ -1442,7 +1609,7 @@ "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": [] }, @@ -1457,7 +1624,7 @@ "output_name": "outfile" }, "input": { - "id": 1, + "id": 2, "output_name": "output" } }, @@ -1467,7 +1634,7 @@ "name": "how" } ], - "label": "Relabelled strand 1", + "label": "Relabelled strand 2", "name": "Relabel identifiers", "outputs": [ { @@ -1476,8 +1643,8 @@ } ], "position": { - "left": 1056, - "top": 176.99999999999994 + "left": 849.9998437853558, + "top": 106 }, "post_job_actions": { "HideDatasetActionoutput": { @@ -1490,7 +1657,7 @@ "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": [] }, @@ -1505,7 +1672,7 @@ "output_name": "outfile" }, "input": { - "id": 2, + "id": 1, "output_name": "output" } }, @@ -1515,7 +1682,7 @@ "name": "how" } ], - "label": "Relabelled strand 2", + "label": "Relabelled strand 1", "name": "Relabel identifiers", "outputs": [ { @@ -1524,8 +1691,8 @@ } ], "position": { - 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