From 3f234aec1668ee426a64669331b1a1f6ae1ea0ba Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Fri, 17 Mar 2023 07:48:35 +0000 Subject: [PATCH 01/22] Updating workflows/transcriptomics/rnaseq-pe from 0.4 to 0.5 --- .../transcriptomics/rnaseq-pe/CHANGELOG.md | 5 + .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 140 ++++++++---------- 2 files changed, 67 insertions(+), 78 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 303c0bfed..83c4dfa28 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.5] 2023-03-17 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2` + ## [0.4] 2023-01-16 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index de3c983aa..ef0e42001 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.4", + "release": "0.5", "name": "RNAseq_PE", "steps": { "0": { @@ -478,7 +478,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2", "errors": null, "id": 13, "input_connections": { @@ -486,10 +486,6 @@ "id": 3, "output_name": "output" }, - "refGenomeSource|GTFconditional|sjdbGTFfile": { - "id": 4, - "output_name": "output" - }, "singlePaired|input": { "id": 7, "output_name": "out_pairs" @@ -510,10 +506,6 @@ { "name": "mapped_reads", "type": "bam" - }, - { - "name": "reads_per_gene", - "type": "tabular" } ], "position": { @@ -527,15 +519,15 @@ "output_name": "splice_junctions" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2", "tool_shed_repository": { - "changeset_revision": "980d2a2e1180", + "changeset_revision": "c7c55b694974", "name": "rgrnastar", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"false\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": \"true\", \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": \"true\", \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbOverhang\": \"99\"}}, \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.7.8a+galaxy1", + "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"Local\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": \"true\", \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": \"true\", \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\"}, \"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"quantmode_output\": {\"__current_case__\": 1, \"quantMode\": \"GeneCounts\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 2, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"quantmode_output\": {\"quantMode\": \"-\", \"__current_case__\": 0}}}, \"singlePaired\": {\"sPaired\": \"paired_collection\", \"__current_case__\": 2, \"input\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "2.7.10b+galaxy2", "type": "tool", "uuid": "49fb2364-339b-4524-befb-c983f97d2a7a", "workflow_outputs": [ @@ -558,9 +550,61 @@ }, "14": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "errors": null, "id": 14, + "input_connections": { + "code": { + "id": 9, + "output_name": "output_param_text" + } + }, + "inputs": [], + "label": "Extract gene counts", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 804.38330078125, + "top": 432.76666259765625 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "HTS count like output" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "tool_shed_repository": { + "changeset_revision": "d698c222f354", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.2", + "type": "tool", + "uuid": "3b5e2b1f-bb92-4b81-8b47-12dc83f81b02", + "workflow_outputs": [ + { + "label": "HTS count like output", + "output_name": "outfile", + "uuid": "41e78153-6863-4b74-abee-4f0f8313c27f" + } + ] + }, + "15": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "errors": null, + "id": 15, "input_connections": { "results_0|software_cond|input": { "id": 7, @@ -569,10 +613,6 @@ "results_1|software_cond|output_0|type|input": { "id": 13, "output_name": "output_log" - }, - "results_1|software_cond|output_1|type|input": { - "id": 13, - "output_name": "reads_per_gene" } }, "inputs": [], @@ -627,62 +667,6 @@ } ] }, - "15": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", - "errors": null, - "id": 15, - "input_connections": { - "code": { - "id": 9, - "output_name": "output_param_text" - }, - "infile": { - "id": 13, - "output_name": "reads_per_gene" - } - }, - "inputs": [], - "label": "Extract gene counts", - "name": "Text reformatting", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 804.38330078125, - "top": 432.76666259765625 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "HTS count like output" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", - "tool_shed_repository": { - "changeset_revision": "d698c222f354", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", - "type": "tool", - "uuid": "3b5e2b1f-bb92-4b81-8b47-12dc83f81b02", - "workflow_outputs": [ - { - "label": "HTS count like output", - "output_name": "outfile", - "uuid": "41e78153-6863-4b74-abee-4f0f8313c27f" - } - ] - }, "16": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1", @@ -996,7 +980,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "a1a923cd89e8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1048,7 +1032,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "a1a923cd89e8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1100,7 +1084,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "a1a923cd89e8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" From 20a4e0a7de26201618c2cfb3a4d3daecc7b25893 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Fri, 17 Mar 2023 07:51:18 +0000 Subject: [PATCH 02/22] Updating workflows/transcriptomics/rnaseq-sr from 0.4 to 0.5 --- .../transcriptomics/rnaseq-sr/CHANGELOG.md | 5 + .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 140 ++++++++---------- 2 files changed, 67 insertions(+), 78 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index eafad0164..79c0a89e3 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -1,5 +1,10 @@ # Changelog +## [0.5] 2023-03-17 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2` + ## [0.4] 2023-01-16 ### Automatic update diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index f91287ff2..bfb4ef1c6 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "RNAseq_SR", - "release": "0.4", + "release": "0.5", "steps": { "0": { "annotation": "Should be a list of single-read RNA-seq fastqs", @@ -448,7 +448,7 @@ }, "12": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2", "errors": null, "id": 12, "input_connections": { @@ -456,10 +456,6 @@ "id": 2, "output_name": "output" }, - "refGenomeSource|GTFconditional|sjdbGTFfile": { - "id": 3, - "output_name": "output" - }, "singlePaired|input1": { "id": 6, "output_name": "out1" @@ -480,10 +476,6 @@ { "name": "mapped_reads", "type": "bam" - }, - { - "name": "reads_per_gene", - "type": "tabular" } ], "position": { @@ -497,15 +489,15 @@ "output_name": "splice_junctions" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2", "tool_shed_repository": { - "changeset_revision": "980d2a2e1180", + "changeset_revision": "c7c55b694974", "name": "rgrnastar", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"algo\": {\"params\": {\"settingsType\": \"full\", \"__current_case__\": 3, \"seed\": {\"seedSearchStartLmax\": \"50\", \"seedSearchStartLmaxOverLread\": \"1.0\", \"seedSearchLmax\": \"0\", \"seedMultimapNmax\": \"10000\", \"seedPerReadNmax\": \"1000\", \"seedPerWindowNmax\": \"50\", \"seedNoneLociPerWindow\": \"10\"}, \"align\": {\"alignIntronMin\": \"20\", \"alignIntronMax\": \"1000000\", \"alignMatesGapMax\": \"1000000\", \"alignSJoverhangMin\": \"8\", \"alignSJstitchMismatchNmax\": {\"alignSJstitchMismatchNmax1\": \"0\", \"alignSJstitchMismatchNmax2\": \"-1\", \"alignSJstitchMismatchNmax3\": \"0\", \"alignSJstitchMismatchNmax4\": \"0\"}, \"alignSJDBoverhangMin\": \"1\", \"alignSplicedMateMapLmin\": \"0\", \"alignSplicedMateMapLminOverLmate\": \"0.66\", \"alignWindowsPerReadNmax\": \"10000\", \"alignTranscriptsPerWindowNmax\": \"100\", \"alignTranscriptsPerReadNmax\": \"10000\", \"alignEndsType\": \"false\", \"peOverlapNbasesMin\": \"0\", \"peOverlapMMp\": \"0.01\"}, \"chim_settings\": {\"chimSegmentMin\": \"12\", \"chimScoreMin\": \"0\", \"chimScoreDropMax\": \"20\", \"chimScoreSeparation\": \"10\", \"chimScoreJunctionNonGTAG\": \"-1\", \"chimJunctionOverhangMin\": \"20\", \"chimSegmentReadGapMax\": \"0\", \"chimFilter\": \"true\", \"chimMainSegmentMultNmax\": \"10\", \"chimMultimapNmax\": \"1\", \"chimMultimapScoreRange\": \"1\"}, \"limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}}, \"chimOutType\": \"\", \"filter\": {\"basic_filters\": [\"exclude_unmapped\"], \"output_params2\": {\"output_select2\": \"yes\", \"__current_case__\": 0, \"outFilterType\": \"true\", \"outFilterMultimapScoreRange\": \"1\", \"outFilterMultimapNmax\": \"20\", \"outFilterMismatchNmax\": \"999\", \"outFilterMismatchNoverLmax\": \"0.3\", \"outFilterMismatchNoverReadLmax\": \"0.04\", \"outFilterScoreMin\": \"0\", \"outFilterScoreMinOverLread\": \"0.66\", \"outFilterMatchNmin\": \"0\", \"outFilterMatchNminOverLread\": \"0.66\", \"outSAMmultNmax\": \"-1\", \"outSAMtlen\": \"1\"}}, \"oformat\": {\"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\"], \"HI_offset\": \"1\", \"outSAMprimaryFlag\": \"OneBestScore\", \"outSAMmapqUnique\": \"255\"}, \"perf\": {\"outBAMsortingBinsN\": \"50\", \"winAnchorMultimapNmax\": \"50\"}, \"quantmode_output\": {\"quantMode\": \"GeneCounts\", \"__current_case__\": 1}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbOverhang\": \"99\"}}, \"singlePaired\": {\"sPaired\": \"single\", \"__current_case__\": 0, \"input1\": {\"__class__\": \"ConnectedValue\"}}, \"twopass\": {\"twopassMode\": \"None\", \"__current_case__\": 0, \"twopass_read_subset\": \"\", \"sj_precalculated\": \"\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", "errors": null, "id": 13, + "input_connections": { + "code": { + "id": 8, + "output_name": "output_param_text" + } + }, + "inputs": [], + "label": "Extract gene counts", + "name": "Text reformatting", + "outputs": [ + { + "name": "outfile", + "type": "input" + } + ], + "position": { + "left": 817.3240254484031, + "top": 423.7625936344438 + }, + "post_job_actions": { + "RenameDatasetActionoutfile": { + "action_arguments": { + "newname": "HTS count like output" + }, + "action_type": "RenameDatasetAction", + "output_name": "outfile" + } + }, + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "tool_shed_repository": { + "changeset_revision": "d698c222f354", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.2", + "type": "tool", + "uuid": "3b5e2b1f-bb92-4b81-8b47-12dc83f81b02", + "workflow_outputs": [ + { + "label": "HTS count like output", + "output_name": "outfile", + "uuid": "799d84a4-0fe4-4ecc-882b-ee007a6f2358" + } + ] + }, + "14": { + "annotation": "", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1", + "errors": null, + "id": 14, "input_connections": { "results_0|software_cond|input": { "id": 6, @@ -539,10 +583,6 @@ "results_1|software_cond|output_0|type|input": { "id": 12, "output_name": "output_log" - }, - "results_1|software_cond|output_1|type|input": { - "id": 12, - "output_name": "reads_per_gene" } }, "inputs": [], @@ -597,62 +637,6 @@ } ] }, - "14": { - "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", - "errors": null, - "id": 14, - "input_connections": { - "code": { - "id": 8, - "output_name": "output_param_text" - }, - "infile": { - "id": 12, - "output_name": "reads_per_gene" - } - }, - "inputs": [], - "label": "Extract gene counts", - "name": "Text reformatting", - "outputs": [ - { - "name": "outfile", - "type": "input" - } - ], - "position": { - "left": 817.3240254484031, - "top": 423.7625936344438 - }, - "post_job_actions": { - "RenameDatasetActionoutfile": { - "action_arguments": { - "newname": "HTS count like output" - }, - "action_type": "RenameDatasetAction", - "output_name": "outfile" - } - }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", - "tool_shed_repository": { - "changeset_revision": "d698c222f354", - "name": "text_processing", - "owner": "bgruening", - "tool_shed": "toolshed.g2.bx.psu.edu" - }, - "tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", - "type": "tool", - "uuid": "3b5e2b1f-bb92-4b81-8b47-12dc83f81b02", - "workflow_outputs": [ - { - "label": "HTS count like output", - "output_name": "outfile", - "uuid": "799d84a4-0fe4-4ecc-882b-ee007a6f2358" - } - ] - }, "15": { "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1", @@ -922,7 +906,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "a1a923cd89e8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -974,7 +958,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "a1a923cd89e8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" @@ -1026,7 +1010,7 @@ }, "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0", "tool_shed_repository": { - "changeset_revision": "07e8b80f278c", + "changeset_revision": "a1a923cd89e8", "name": "bedtools", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" From 7840e21ff7de1eb0e42f55c92a0fb4c3d7e5aa0b Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 17 Apr 2023 07:49:37 +0000 Subject: [PATCH 03/22] Updating workflows/transcriptomics/rnaseq-pe from 0.5 to 0.6 --- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 55 ++++++++++++++----- 1 file changed, 41 insertions(+), 14 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index ef0e42001..c35aee307 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.5", + "release": "0.6", "name": "RNAseq_PE", "steps": { "0": { @@ -37,6 +37,7 @@ "tool_version": null, "type": "data_collection_input", "uuid": "688da967-e739-409a-b950-b4e4985a1a3b", + "when": null, "workflow_outputs": [] }, "1": { @@ -63,6 +64,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "0179b655-f7e2-4b8b-b8b1-f875d0d8039f", + "when": null, "workflow_outputs": [] }, "2": { @@ -89,6 +91,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "2cf82136-4f80-43f5-bf2d-fde510bf8a93", + "when": null, "workflow_outputs": [] }, "3": { @@ -115,6 +118,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "ff4a9932-6ed0-436f-a63c-d6fbe2a582a3", + "when": null, "workflow_outputs": [] }, "4": { @@ -141,6 +145,7 @@ "tool_version": null, "type": "data_input", "uuid": "c91756d4-f7f1-4dcc-97f6-da4c96a53c94", + "when": null, "workflow_outputs": [] }, "5": { @@ -167,6 +172,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "fd2c51fd-58b3-43b5-b8ce-a919f5325cb7", + "when": null, "workflow_outputs": [] }, "6": { @@ -193,6 +199,7 @@ "tool_version": null, "type": "data_input", "uuid": "cc52d397-17a9-4c38-85f6-a7c0b8f21985", + "when": null, "workflow_outputs": [] }, "7": { @@ -250,10 +257,11 @@ "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"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: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": \"false\"}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source2\": {\"adapter_source_list2\": \"user\", \"__current_case__\": 0, \"adapter_name2\": \"Please use: For R2: - 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"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_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+galaxy1", "type": "tool", "uuid": "e39f8468-742e-4cc7-8b29-3955c4adb0d0", + "when": null, "workflow_outputs": [] }, "17": { @@ -762,6 +779,7 @@ "tool_version": "1.1.2", "type": "tool", "uuid": "bf5398ae-c2a2-4545-bee1-29f2f77b4e3e", + "when": null, "workflow_outputs": [] }, "18": { @@ -844,10 +862,11 @@ "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_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", "type": "tool", "uuid": "a3371ab0-86dd-4302-bdbc-4e79421186d9", + "when": null, "workflow_outputs": [ { "label": "genes_expression", @@ -903,6 +922,7 @@ "tool_version": "0.0.2", "type": "tool", "uuid": "405ecc3a-86fc-4371-8857-5f5c13d35360", + "when": null, "workflow_outputs": [] }, "20": { @@ -937,10 +957,11 @@ } }, "tool_id": "param_value_from_file", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"float\", \"remove_newlines\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"float\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.0", "type": "tool", "uuid": "f703b0e5-d079-4428-8850-9e0dac01a2f9", + "when": null, "workflow_outputs": [] }, "21": { @@ -985,10 +1006,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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_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": "2.30.0", "type": "tool", "uuid": "da5b255c-7906-4c1d-954a-5dbac6c40e30", + "when": null, "workflow_outputs": [] }, "22": { @@ -1037,10 +1059,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.30.0", "type": "tool", "uuid": "2949dec8-08e1-47d8-a046-b10f601b4e4f", + "when": null, "workflow_outputs": [] }, "23": { @@ -1089,10 +1112,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.30.0", "type": "tool", "uuid": "109391e9-3f11-4003-86cb-5997860ce259", + "when": null, "workflow_outputs": [] }, "24": { @@ -1133,6 +1157,7 @@ "tool_version": "1.1.1", "type": "tool", "uuid": "164a4c62-2e72-4090-b645-4cf55b803336", + "when": null, "workflow_outputs": [ { "label": "both strands coverage", @@ -1179,6 +1204,7 @@ "tool_version": "1.1.1", "type": "tool", "uuid": "5c7b4f5f-50d1-4050-a40c-43d075c84779", + "when": null, "workflow_outputs": [ { "label": "positive strand coverage", @@ -1225,6 +1251,7 @@ "tool_version": "1.1.1", "type": "tool", "uuid": "852c1da8-6826-4a58-afc7-7eb26b668f00", + "when": null, "workflow_outputs": [ { "label": "negative strand coverage", From 272dae8a183168a390b03f21e2fae27a35bad873 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Mon, 17 Apr 2023 07:52:15 +0000 Subject: [PATCH 04/22] Updating workflows/transcriptomics/rnaseq-sr from 0.5 to 0.6 --- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 53 ++++++++++++++----- 1 file changed, 39 insertions(+), 14 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index bfb4ef1c6..b47cd1df8 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "RNAseq_SR", - "release": "0.5", + "release": "0.6", "steps": { "0": { "annotation": "Should be a list of single-read RNA-seq fastqs", @@ -37,6 +37,7 @@ "tool_version": null, "type": "data_collection_input", "uuid": "688da967-e739-409a-b950-b4e4985a1a3b", + "when": null, "workflow_outputs": [] }, "1": { @@ -63,6 +64,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "0179b655-f7e2-4b8b-b8b1-f875d0d8039f", + "when": null, "workflow_outputs": [] }, "2": { @@ -89,6 +91,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "ff4a9932-6ed0-436f-a63c-d6fbe2a582a3", + "when": null, "workflow_outputs": [] }, "3": { @@ -115,6 +118,7 @@ "tool_version": null, "type": "data_input", "uuid": "c91756d4-f7f1-4dcc-97f6-da4c96a53c94", + "when": null, "workflow_outputs": [] }, "4": { @@ -141,6 +145,7 @@ "tool_version": null, "type": "parameter_input", "uuid": "fd2c51fd-58b3-43b5-b8ce-a919f5325cb7", + "when": null, "workflow_outputs": [] }, "5": { @@ -167,6 +172,7 @@ "tool_version": null, "type": "data_input", "uuid": "cc52d397-17a9-4c38-85f6-a7c0b8f21985", + "when": null, "workflow_outputs": [] }, "6": { @@ -220,10 +226,11 @@ "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": \"false\", \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": \"false\"}, \"filter_options\": {\"discard_trimmed\": \"false\", \"discard_untrimmed\": \"false\", \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": \"false\"}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": \"false\"}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": \"false\", \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": \"false\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"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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"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_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+galaxy1", "type": "tool", "uuid": "e39f8468-742e-4cc7-8b29-3955c4adb0d0", + "when": null, "workflow_outputs": [] }, "16": { @@ -732,6 +748,7 @@ "tool_version": "1.1.2", "type": "tool", "uuid": "bf5398ae-c2a2-4545-bee1-29f2f77b4e3e", + "when": null, "workflow_outputs": [] }, "17": { @@ -814,10 +831,11 @@ "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_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", "type": "tool", "uuid": "a3371ab0-86dd-4302-bdbc-4e79421186d9", + "when": null, "workflow_outputs": [ { "label": "transcripts_expression", @@ -863,10 +881,11 @@ } }, "tool_id": "param_value_from_file", - "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"float\", \"remove_newlines\": \"true\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_state": "{\"input1\": {\"__class__\": \"ConnectedValue\"}, \"param_type\": \"float\", \"remove_newlines\": true, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "0.1.0", "type": "tool", "uuid": "f703b0e5-d079-4428-8850-9e0dac01a2f9", + "when": null, "workflow_outputs": [] }, "19": { @@ -911,10 +930,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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_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": "2.30.0", "type": "tool", "uuid": "da5b255c-7906-4c1d-954a-5dbac6c40e30", + "when": null, "workflow_outputs": [] }, "20": { @@ -963,10 +983,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.30.0", "type": "tool", "uuid": "2949dec8-08e1-47d8-a046-b10f601b4e4f", + "when": null, "workflow_outputs": [] }, "21": { @@ -1015,10 +1036,11 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": \"false\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "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\": {\"__class__\": \"ConnectedValue\"}, \"three\": false, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.30.0", "type": "tool", "uuid": "109391e9-3f11-4003-86cb-5997860ce259", + "when": null, "workflow_outputs": [] }, "22": { @@ -1059,6 +1081,7 @@ "tool_version": "1.1.1", "type": "tool", "uuid": "164a4c62-2e72-4090-b645-4cf55b803336", + "when": null, "workflow_outputs": [ { "label": "both strands coverage", @@ -1105,6 +1128,7 @@ "tool_version": "1.1.1", "type": "tool", "uuid": "5c7b4f5f-50d1-4050-a40c-43d075c84779", + "when": null, "workflow_outputs": [ { "label": "positive strand coverage", @@ -1151,6 +1175,7 @@ "tool_version": "1.1.1", "type": "tool", "uuid": "852c1da8-6826-4a58-afc7-7eb26b668f00", + "when": null, "workflow_outputs": [ { "label": "negative strand coverage", From 18798b3443a25988384838f15726f99c2e56494b Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Sat, 17 Jun 2023 07:47:09 +0000 Subject: [PATCH 05/22] Updating workflows/transcriptomics/rnaseq-pe from 0.6 to 0.7 --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index c35aee307..bb40cb37d 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.6", + "release": "0.7", "name": "RNAseq_PE", "steps": { "0": { @@ -204,7 +204,7 @@ }, "7": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", "errors": null, "id": 7, "input_connections": { @@ -250,15 +250,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "135b80fb1ac2", + "changeset_revision": "8c0175e03cee", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"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: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}, \"r2\": {\"adapters2\": [{\"__index__\": 0, \"adapter_source2\": {\"adapter_source_list2\": \"user\", \"__current_case__\": 0, \"adapter_name2\": \"Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT\", \"adapter2\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters2\": [], \"anywhere_adapters2\": [], \"cut2\": \"0\", \"quality_cutoff2\": \"\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0+galaxy1", + "tool_version": "4.4+galaxy0", "type": "tool", "uuid": "7f7ca59a-09db-491f-b185-1caa51e9d2aa", "when": null, From 10a4df47e9d5de76bfbf51a291d7de1179a68385 Mon Sep 17 00:00:00 2001 From: planemo-autoupdate Date: Sat, 17 Jun 2023 07:49:24 +0000 Subject: [PATCH 06/22] Updating workflows/transcriptomics/rnaseq-sr from 0.6 to 0.7 --- workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index b47cd1df8..c836d0728 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "RNAseq_SR", - "release": "0.6", + "release": "0.7", "steps": { "0": { "annotation": "Should be a list of single-read RNA-seq fastqs", @@ -177,7 +177,7 @@ }, "6": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", + "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", "errors": null, "id": 6, "input_connections": { @@ -219,15 +219,15 @@ "output_name": "report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1", + "tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.4+galaxy0", "tool_shed_repository": { - "changeset_revision": "135b80fb1ac2", + "changeset_revision": "8c0175e03cee", "name": "cutadapt", "owner": "lparsons", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"__job_resource\": {\"__current_case__\": 0, \"__job_resource__select\": \"no\"}, \"adapter_options\": {\"action\": \"trim\", \"internal\": \"\", \"error_rate\": \"0.1\", \"no_indels\": false, \"times\": \"1\", \"overlap\": \"3\", \"match_read_wildcards\": \" \", \"revcomp\": false}, \"filter_options\": {\"discard_trimmed\": false, \"discard_untrimmed\": false, \"minimum_length\": \"15\", \"maximum_length\": null, \"length_R2_options\": {\"length_R2_status\": \"False\", \"__current_case__\": 1}, \"max_n\": null, \"pair_filter\": \"any\", \"max_expected_errors\": null, \"discard_cassava\": false}, \"library\": {\"type\": \"single\", \"__current_case__\": 0, \"input_1\": {\"__class__\": \"ConnectedValue\"}, \"r1\": {\"adapters\": [{\"__index__\": 0, \"adapter_source\": {\"adapter_source_list\": \"user\", \"__current_case__\": 0, \"adapter_name\": \"Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC\", \"adapter\": {\"__class__\": \"ConnectedValue\"}}, \"single_noindels\": false}], \"front_adapters\": [], \"anywhere_adapters\": [], \"cut\": \"0\"}}, \"output_selector\": [\"report\"], \"read_mod_options\": {\"quality_cutoff\": \"30\", \"nextseq_trim\": \"0\", \"trim_n\": false, \"strip_suffix\": \"\", \"shorten_options\": {\"shorten_values\": \"False\", \"__current_case__\": 1}, \"length_tag\": \"\", \"rename\": \"\", \"zero_cap\": false}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "4.0+galaxy1", + "tool_version": "4.4+galaxy0", "type": "tool", "uuid": "7f7ca59a-09db-491f-b185-1caa51e9d2aa", "when": null, From 9ab9fa41b468c231423a3ec684418f067c341afe Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 30 Aug 2023 07:27:14 +0200 Subject: [PATCH 07/22] update dockstore --- workflows/transcriptomics/rnaseq-sr/.dockstore.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/workflows/transcriptomics/rnaseq-sr/.dockstore.yml b/workflows/transcriptomics/rnaseq-sr/.dockstore.yml index 4b542ec01..61f298b5c 100644 --- a/workflows/transcriptomics/rnaseq-sr/.dockstore.yml +++ b/workflows/transcriptomics/rnaseq-sr/.dockstore.yml @@ -1,7 +1,11 @@ version: 1.2 workflows: - name: main - primaryDescriptorPath: /rnaseq-sr.ga subclass: Galaxy + publish: true + primaryDescriptorPath: /rnaseq-sr.ga testParameterFiles: - /rnaseq-sr-tests.yml + authors: + - name: Lucille Delisle + orcid: 0000-0002-1964-4960 From 1a8ee07429d6eb49b8ae522c7371a34748274c3a Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 30 Aug 2023 07:29:26 +0200 Subject: [PATCH 08/22] synchronize version and changelog --- workflows/transcriptomics/rnaseq-sr/CHANGELOG.md | 2 +- workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index 79c0a89e3..7dbd00111 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -3,7 +3,7 @@ ## [0.5] 2023-03-17 ### Automatic update -- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3` ## [0.4] 2023-01-16 diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index c836d0728..9965b1454 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -11,7 +11,7 @@ "format-version": "0.1", "license": "MIT", "name": "RNAseq_SR", - "release": "0.7", + "release": "0.5", "steps": { "0": { "annotation": "Should be a list of single-read RNA-seq fastqs", From 3a68d546036dd5bf5e5383be2563612c937b983f Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Wed, 30 Aug 2023 18:41:33 +0200 Subject: [PATCH 09/22] try to update workflow --- .../rnaseq-sr/rnaseq-sr-tests.yml | 19 +- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 2062 ++++++++++++----- 2 files changed, 1530 insertions(+), 551 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 86eefc13d..20d11beed 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -14,6 +14,9 @@ forward_adapter: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC reference_genome: dm6 strandness: unstranded + split coverage by strand: false + cufflinks_FPKM: true + stringtie_FPKM: true outputs: output_log: element_tests: @@ -72,13 +75,13 @@ asserts: has_text: text: "FBgn0010247\t14" - transcripts_expression: + transcripts_expression_cufflinks: element_tests: GSM461177: asserts: has_text: text: "FBtr0078104\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t1583\t0.626702\t18.291\t9.78604\t26.796\tOK" - genes_expression: + genes_expression_cufflinks: element_tests: GSM461177: asserts: @@ -90,15 +93,3 @@ has_size: value: 6075761 delta: 600000 - negative strand coverage: - element_tests: - GSM461177: - has_size: - value: 3103918 - delta: 300000 - positive strand coverage: - element_tests: - GSM461177: - has_size: - value: 3103918 - delta: 300000 diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index 9965b1454..2bf8cd853 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -29,8 +29,8 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, - "top": 212.8770301624129 + "left": 0, + "top": 274.77146559574123 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", @@ -56,8 +56,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 43.890171980359995, - "top": 285.8662262316923 + "left": 15.45001220703125, + "top": 335.3214839062881 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", @@ -83,8 +83,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 85.96286640919556, - "top": 377.90023201856144 + "left": 32.63336181640625, + "top": 423.53809767581936 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -110,8 +110,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 123.78189901188189, - "top": 469.9149430489595 + "left": 50.60003662109375, + "top": 508.15479689456936 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -137,8 +137,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 170.8429960529655, - "top": 554.9304192138105 + "left": 81.25, + "top": 568.5214961133194 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - 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991.8020297092517 - }, - "post_job_actions": { - "RenameDatasetActionout_file1": { - "action_arguments": { - "newname": "negative strand coverage" - }, - "action_type": "RenameDatasetAction", - "output_name": "out_file1" - } + "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2", + "tool_shed_repository": { + "changeset_revision": "ddf54b12c295", + "name": "text_processing", + "owner": "bgruening", + "tool_shed": "toolshed.g2.bx.psu.edu" }, - "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", + "tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.1.2", "type": "tool", - "uuid": "852c1da8-6826-4a58-afc7-7eb26b668f00", + "uuid": "3b5e2b1f-bb92-4b81-8b47-12dc83f81b02", "when": null, "workflow_outputs": [ { - "label": "negative strand coverage", - "output_name": "out_file1", - "uuid": "5606e5e4-9519-4e3a-8254-09f7263ccdaa" + "label": "HTS count like output", + "output_name": "outfile", + "uuid": "799d84a4-0fe4-4ecc-882b-ee007a6f2358" } ] } @@ -1188,6 +2176,6 @@ "tags": [ "RNAseq" ], - "uuid": "49f297ff-5c0b-4efb-b696-ae25868f668a", - "version": 2 + "uuid": "8ebdc332-ed3b-4d43-8301-33da8eefb9d3", + "version": 17 } \ No newline at end of file From 1cf96a60e86e27e535d8bed34c54260f4b2686d3 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Fri, 1 Sep 2023 18:02:52 +0200 Subject: [PATCH 10/22] update test for stringtie --- workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 20d11beed..88b4c4a3f 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -87,6 +87,12 @@ asserts: has_text: text: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t32.1015\t22.1771\t42.0259\tOK" + genes_expression_stringtie: + element_tests: + GSM461177: + asserts: + has_text: + text: "FBgn0031217 CG11377 chr2L + 102380 104142 1.003790 31.826454 55.206604" both strands coverage: element_tests: GSM461177: From 35e0856b5c4f8d32fdb27f2a27e403d31fabb0a9 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 4 Sep 2023 17:57:41 +0200 Subject: [PATCH 11/22] update workflow and tests --- .../rnaseq-pe/rnaseq-pe-tests.yml | 35 +- .../transcriptomics/rnaseq-pe/rnaseq-pe.ga | 2109 ++++++++++++----- 2 files changed, 1534 insertions(+), 610 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 60938685e..9952cd786 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -24,6 +24,9 @@ reverse_adapter: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT reference_genome: dm6 strandness: unstranded + split coverage by strand: true + cufflinks_FPKM: false + stringtie_FPKM: true outputs: output_log: element_tests: @@ -82,33 +85,19 @@ asserts: has_text: text: "FBgn0010247\t13" - transcripts_expression: + stranded coverage: element_tests: - GSM461177: - asserts: - has_text: - text: "FBtr0078104\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t1583\t1.95689 28.9556 19.9177 37.9936\tOK" - genes_expression: - element_tests: - GSM461177: - asserts: - has_text: - text: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t28.9556 19.7218 38.1895\tOK" - both strands coverage: - element_tests: - GSM461177: - has_size: - value: 9885639 - delta: 900000 - negative strand coverage: - element_tests: - GSM461177: + GSM461177_reverse: has_size: value: 7756965 delta: 700000 - positive strand coverage: - element_tests: - GSM461177: + GSM461177_forward: has_size: value: 7756965 delta: 700000 + genes_expression_stringtie: + element_tests: + GSM461177: + asserts: + has_text: + text: "FBgn0031217 CG11377 chr2L + 102380 104142 1.003790 31.826454 55.206604" diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index bb40cb37d..f433a049d 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,6 +1,6 @@ { "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. The counts are reprocess to be similar to HTSeq-count output. FPKM are computed with cufflinks. Coverage (per million mapped reads) are computed with bedtools on uniquely mapped reads (with R2 orientation inverted).", + "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.", "creator": [ { "class": "Person", @@ -10,7 +10,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.7", + "release": "0.5", "name": "RNAseq_PE", "steps": { "0": { @@ -30,7 +30,7 @@ "outputs": [], "position": { "left": 0, - "top": 198.9666748046875 + "top": 154.21153644287114 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -56,8 +56,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 16.916671752929688, - "top": 271.8833312988281 + "left": 26.45001220703125, + "top": 240.31154254638676 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", @@ -83,14 +83,14 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 51, - "top": 361.8999938964844 + "left": 68, + "top": 328.4448738452149 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", "tool_version": null, "type": "parameter_input", - 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Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 11 Sep 2023 15:50:00 +0200 Subject: [PATCH 13/22] update changelog and tests --- workflows/transcriptomics/rnaseq-pe/CHANGELOG.md | 7 ++++++- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index 83c4dfa28..e772b7712 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -3,7 +3,12 @@ ## [0.5] 2023-03-17 ### Automatic update -- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy2` +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` + +### Manual update +- Use STAR to compute normalized strand splitted coverage +- Propose StringTie to compute FPKM etc... +- Put cufflinks step optional ## [0.4] 2023-01-16 diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 9952cd786..a4dc67444 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -24,7 +24,6 @@ reverse_adapter: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT reference_genome: dm6 strandness: unstranded - split coverage by strand: true cufflinks_FPKM: false stringtie_FPKM: true outputs: @@ -85,6 +84,12 @@ asserts: has_text: text: "FBgn0010247\t13" + both strands coverage: + element_tests: + GSM461177: + has_size: + value: 9885639 + delta: 900000 stranded coverage: element_tests: GSM461177_reverse: From 81ef81549cb95b153dcdcaffa1a34b7a8ba064df Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 11 Sep 2023 15:57:39 +0200 Subject: [PATCH 14/22] Update README --- workflows/transcriptomics/rnaseq-pe/README.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/README.md b/workflows/transcriptomics/rnaseq-pe/README.md index c912714bd..17271928d 100644 --- a/workflows/transcriptomics/rnaseq-pe/README.md +++ b/workflows/transcriptomics/rnaseq-pe/README.md @@ -17,16 +17,19 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM - adapter sequences: this depends on the library preparation. Usually classical 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. - reference_genome: this field will be adapted to the genomes available for STAR -- strandness: 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. This will help you to get from STAR only the counts corresponding to your library preparation. This is also used for the stranded coverage and for FPKM computation with cufflinks. +- strandness: 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. This will help you to get from STAR only the counts corresponding to your library preparation. 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 Cufflinks. ## 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. +- 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 stranded specific normalized coverage (on uniquely mapped reads). - A multiQC is run to have an overview of the QC. This can also be used to get the strandness. -- FPKM values for reads and transcripts are computed with cufflinks using correction for multi-mapped reads. +- FPKM values for tenes and transcripts are computed with cufflinks using correction for multi-mapped reads (optionnal). +- FPKM/TMP values for genes are computed with SstringTie. - The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1). -- Coverage unstranded, and each strand independently is computed with bedtools and normalized to the number of million uniquely mapped reads (in order to compute stranded coverage the BAM is modified so second mate in pairs matches orientation of the first mate in pairs). +- Coverage unstranded is computed with bedtools and normalized to the number of million uniquely mapped reads. - The three coverage files are converted to bigwig. ### Warning From a114979815e6c45262d1830cc0c7d02aec89462e Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 11 Sep 2023 16:04:45 +0200 Subject: [PATCH 15/22] update workflow --- .../transcriptomics/rnaseq-sr/rnaseq-sr.ga | 2191 +++++++---------- 1 file changed, 907 insertions(+), 1284 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index 2bf8cd853..bd159c3f9 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of single-read fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously. The counts are reprocess to be similar to HTSeq-count output. FPKM are computed with cufflinks. Coverage (per million mapped reads) are computed with bedtools on uniquely mapped reads.", + "annotation": "This workflow takes as input a list of single-reads 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.", "creator": [ { "class": "Person", @@ -30,13 +30,13 @@ "outputs": [], "position": { "left": 0, - "top": 274.77146559574123 + "top": 354 }, "tool_id": null, - "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list\"}", + "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "688da967-e739-409a-b950-b4e4985a1a3b", + "uuid": "633ddb66-8a2b-4822-b894-2e947bf6607b", "when": null, "workflow_outputs": [] }, @@ -56,8 +56,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 15.45001220703125, - "top": 335.3214839062881 + "left": 42.45001220703125, + "top": 430.91668701171875 }, "tool_id": null, "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}", @@ -83,8 +83,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 32.63336181640625, - "top": 423.53809767581936 + "left": 107.63336181640625, + "top": 522.134886401586 }, "tool_id": null, "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}", @@ -110,8 +110,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 50.60003662109375, - "top": 508.15479689456936 + "left": 125.60003662109375, + "top": 606.751585620336 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\"}", @@ -137,8 +137,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 81.25, - "top": 568.5214961133194 + "left": 156.25, + "top": 667.118284839086 }, "tool_id": null, "tool_state": "{\"restrictions\": [\"stranded - forward\", \"stranded - reverse\", \"unstranded\"], \"parameter_type\": \"text\", \"optional\": false}", @@ -149,37 +149,10 @@ "workflow_outputs": [] }, "5": { - "annotation": "Whether coverage should be for forward and reverse separated", - "content_id": null, - "errors": null, - "id": 5, - "input_connections": {}, - "inputs": [ - { - 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+175,11 @@ "when": null, "workflow_outputs": [] }, - "7": { + "6": { "annotation": "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": [ { @@ -218,8 +191,8 @@ "name": "Input dataset", "outputs": [], "position": { - "left": 154.7333984375, - "top": 780.0047724805069 + "left": 201.73333740234375, + "top": 809.5967887257666 }, "tool_id": null, "tool_state": "{\"optional\": true, \"tag\": \"\"}", @@ -229,11 +202,11 @@ "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": [ { @@ -245,8 +218,8 @@ "name": "Input parameter", "outputs": [], "position": { - "left": 181.88330078125, - "top": 882.8214228711319 + "left": 245.88330078125, + "top": 926.4134391163916 }, "tool_id": null, 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"tool_state": "{\"code\": {\"__class__\": \"ConnectedValue\"}, \"infile\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.1.2", - "type": "tool", - "uuid": "3b5e2b1f-bb92-4b81-8b47-12dc83f81b02", - "when": null, - "workflow_outputs": [ - { - "label": "HTS count like output", - "output_name": "outfile", - "uuid": "799d84a4-0fe4-4ecc-882b-ee007a6f2358" - } - ] } }, "tags": [ "RNAseq" ], - "uuid": "8ebdc332-ed3b-4d43-8301-33da8eefb9d3", - "version": 17 + "uuid": "1097b24d-c228-4d2c-908d-4220eb5fc3e7", + "version": 5 } \ No newline at end of file From 1ce395a572f6026a649e5f19b635a4bd3abd0bdb Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 11 Sep 2023 16:10:24 +0200 Subject: [PATCH 16/22] update README tests etc... --- workflows/transcriptomics/rnaseq-sr/CHANGELOG.md | 7 ++++++- workflows/transcriptomics/rnaseq-sr/README.md | 11 +++++++---- .../transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml | 11 ++++++++++- 3 files changed, 23 insertions(+), 6 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index 7dbd00111..53778ac2f 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -3,7 +3,12 @@ ## [0.5] 2023-03-17 ### Automatic update -- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` + +### Manual update +- Use STAR to compute normalized strand splitted coverage +- Propose StringTie to compute FPKM etc... +- Put cufflinks step optional ## [0.4] 2023-01-16 diff --git a/workflows/transcriptomics/rnaseq-sr/README.md b/workflows/transcriptomics/rnaseq-sr/README.md index 7340d24e5..4f2a8819a 100644 --- a/workflows/transcriptomics/rnaseq-sr/README.md +++ b/workflows/transcriptomics/rnaseq-sr/README.md @@ -17,14 +17,17 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM - forward adapter sequence: this depends on the library preparation. Usually classical 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. - reference_genome: this field will be adapted to the genomes available for STAR -- strandness: 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. This will help you to get from STAR only the counts corresponding to your library preparation. This is also used for the stranded coverage and for FPKM computation with cufflinks. +- strandness: 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. This will help you to get from STAR only the counts corresponding to your library preparation. 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 Cufflinks. ## 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. +- 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 stranded specific normalized coverage (on uniquely mapped reads). - A multiQC is run to have an overview of the QC. This can also be used to get the strandness. -- FPKM values for reads and transcripts are computed with cufflinks using correction for multi-mapped reads. +- FPKM values for tenes and transcripts are computed with cufflinks using correction for multi-mapped reads (optionnal). +- FPKM/TMP values for genes are computed with SstringTie. - The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1). - Coverage unstranded, and each strand independently is computed with bedtools and normalized to the number of million uniquely mapped reads. - The three coverage files are converted to bigwig. @@ -34,7 +37,7 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM - The coverage stranded output depends on the strandness of the library: - If you have an unstranded library, stranded coverages are useless - If you have a forward stranded library, the label matches the orientation of reads. - - If you have a reverse stranded library, `positive strand coverage` should correspond to genes on the forward strand and uses the reads mapped on the reverse strand. `negative strand coverage` should correspond to genes on the reverse strand and uses the reads mapped on the forward strand. + - If you have a reverse stranded library, `forward` should correspond to genes on the forward strand and uses the reads mapped on the reverse strand. `reverse` should correspond to genes on the reverse strand and uses the reads mapped on the forward strand. ## Contribution diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 88b4c4a3f..f2daf61ff 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -14,7 +14,6 @@ forward_adapter: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC reference_genome: dm6 strandness: unstranded - split coverage by strand: false cufflinks_FPKM: true stringtie_FPKM: true outputs: @@ -99,3 +98,13 @@ has_size: value: 6075761 delta: 600000 + stranded coverage: + element_tests: + GSM461177_reverse: + has_size: + value: 3103918 + delta: 300000 + GSM461177_forward: + has_size: + value: 3103918 + delta: 300000 From f91afa6d93ab74d2ec5cc6ae1a6aa68d3862aaee Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Mon, 11 Sep 2023 23:18:26 +0200 Subject: [PATCH 17/22] update test results --- .../transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index f2daf61ff..76b13e4d2 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -26,7 +26,7 @@ - that: "has_text" text: "Uniquely mapped reads number |\t871202" - that: "has_text" - text: "Number of reads mapped to multiple loci |\t91809" + text: "Number of reads mapped to multiple loci |\t91808" mapped-reads: element_tests: GSM461177: @@ -39,7 +39,7 @@ cutadapt: asserts: has_text: - text: "GSM461177\t4.0\t1057657\t25033\t6191\t1051466\t39133309\t1439589\t37547108\t4.053327051898423" + text: "GSM461177\t4.4\t1057657\t25033\t6191\t1051466\t39133309\t1439589\t37547108\t4.053327051898423" general_stats: asserts: has_text: @@ -79,19 +79,19 @@ GSM461177: asserts: has_text: - text: "FBtr0078104\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t1583\t0.626702\t18.291\t9.78604\t26.796\tOK" + text: "FBtr0078104\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t1583\t0.626702\t18.291\t9.78605\t26.796\tOK" genes_expression_cufflinks: element_tests: GSM461177: asserts: has_text: - text: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t32.1015\t22.1771\t42.0259\tOK" + text: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t32.1016\t22.1771\t42.0259\tOK" genes_expression_stringtie: element_tests: GSM461177: asserts: has_text: - text: "FBgn0031217 CG11377 chr2L + 102380 104142 1.003790 31.826454 55.206604" + text: "FBgn0031217 CG11377 chr2L + 102380 104142 0.994315 32.391769 56.255165" both strands coverage: element_tests: GSM461177: From 5141c089d6bc29e7991b4f305e4a426e68efe79b Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Tue, 12 Sep 2023 09:30:55 +0200 Subject: [PATCH 18/22] use regex on tests --- .../transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 76b13e4d2..437281102 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -50,8 +50,8 @@ n: 4 star: asserts: - has_text: - text: "GSM461177\t1051466.0\t35.0\t871202.0\t82.86\t35.4\t51184.0\t50995.0\t50810.0\t343.0\t12.0\t19.0\t0.48\t0.0\t1.48\t0.0\t1.36\t91809.0\t8.73\t34515.0\t3.28\t0.0\t4.76\t0.37\t0\t50050\t3890" + has_text_matching: + expression: "GSM461177\t1051466.0\t35.0\t871202.0\t82.86\t35.4\t51184.0\t50995.0\t50810.0\t343.0\t12.0\t19.0\t0.48\t0.0\t1.48\t0.0\t1.36\t9180[89].0\t8.73\t34515.0\t3.28\t0.0\t4.76\t0.37\t0\t5005[01]\t3890" MultiQC webpage: asserts: - that: "has_text" @@ -84,14 +84,14 @@ element_tests: GSM461177: asserts: - has_text: - text: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t32.1016\t22.1771\t42.0259\tOK" + has_text_matching: + expression: "FBgn0031217\t-\t-\tFBgn0031217\tCG11377\t-\tchr2L:102379-104142\t-\t-\t32.1016\t22.1771\t42.02[0-9]*\tOK" genes_expression_stringtie: element_tests: GSM461177: asserts: has_text: - text: "FBgn0031217 CG11377 chr2L + 102380 104142 0.994315 32.391769 56.255165" + text: "FBgn0031217\tCG11377\tchr2L\t+\t102380\t104142\t0.994315\t32.391769\t56.255165" both strands coverage: element_tests: GSM461177: From 21c26456065b0f3e0023ea1a18e65e7f996994f8 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Tue, 12 Sep 2023 12:47:18 +0200 Subject: [PATCH 19/22] fix spelling --- workflows/transcriptomics/rnaseq-pe/README.md | 14 +++++++------- workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga | 2 +- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/README.md b/workflows/transcriptomics/rnaseq-pe/README.md index 17271928d..bfffd01fc 100644 --- a/workflows/transcriptomics/rnaseq-pe/README.md +++ b/workflows/transcriptomics/rnaseq-pe/README.md @@ -15,19 +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 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. +- 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 -- strandness: 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. This will help you to get from STAR only the counts corresponding to your library preparation. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. +- strandness: For stranded RNA, reverse means that the first read in pair is complementary to the coding sequence, forward means that the first read in pair is in the same orientation as the coding sequence. This will help you to get from STAR only the counts corresponding to your library preparation. 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 Cufflinks. +- 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 stranded specific normalized coverage (on uniquely mapped reads). +- 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 stranded specific normalized coverage (on uniquely mapped reads). - A multiQC is run to have an overview of the QC. This can also be used to get the strandness. -- FPKM values for tenes and transcripts are computed with cufflinks using correction for multi-mapped reads (optionnal). -- FPKM/TMP values for genes are computed with SstringTie. +- 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. - The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1). - Coverage unstranded 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 d7494904c..3b7deb7c5 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -1,6 +1,6 @@ { "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.", + "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.", "creator": [ { "class": "Person", From 3457a6299f61bd764585caf5cde0246355b1b9ed Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Tue, 12 Sep 2023 12:42:12 +0200 Subject: [PATCH 20/22] check spelling --- workflows/transcriptomics/rnaseq-sr/README.md | 16 ++++++++-------- workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-sr/README.md b/workflows/transcriptomics/rnaseq-sr/README.md index 4f2a8819a..7a7cc1064 100644 --- a/workflows/transcriptomics/rnaseq-sr/README.md +++ b/workflows/transcriptomics/rnaseq-sr/README.md @@ -2,7 +2,7 @@ ## Inputs dataset -- The workflow needs a list of dataset of fastqsanger. +- The workflow needs a list of datasets of fastqsanger. - As well as a gtf file with genes - Optional, but recommended: a gtf file with regions to exclude from normalization in Cufflinks. @@ -15,21 +15,21 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM ## Inputs values -- forward adapter sequence: this depends on the library preparation. Usually classical 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. +- forward adapter sequence: 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 - strandness: 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. This will help you to get from STAR only the counts corresponding to your library preparation. 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 Cufflinks. +- 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 stranded specific normalized coverage (on uniquely mapped reads). +- 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 stranded specific normalized coverage (on uniquely mapped reads). - A multiQC is run to have an overview of the QC. This can also be used to get the strandness. -- FPKM values for tenes and transcripts are computed with cufflinks using correction for multi-mapped reads (optionnal). -- FPKM/TMP values for genes are computed with SstringTie. +- 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 (this step is optional). - The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1). -- Coverage unstranded, and each strand independently is computed with bedtools and normalized to the number of million uniquely mapped reads. +- Coverage unstranded is computed with bedtools and normalized to the number of million uniquely mapped reads. - The three coverage files are converted to bigwig. ### Warning diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index bd159c3f9..d34262c4c 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -1,6 +1,6 @@ { "a_galaxy_workflow": "true", - "annotation": "This workflow takes as input a list of single-reads 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.", + "annotation": "This workflow takes as input a list of single-reads 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.", "creator": [ { "class": "Person", From 0e6c447ef755a8b93ee241b6cbd4b9b924343ad2 Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Thu, 14 Sep 2023 22:22:05 +0200 Subject: [PATCH 21/22] fix tests --- workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index a4dc67444..3e43a8bb9 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -49,7 +49,7 @@ cutadapt: asserts: has_text: - text: "GSM461177_2 4.0 1057657 25033 25779 25250 1032407 78266618 3650637 73538382 6.041191149974054" + text: "GSM461177_2 4.4 1057657 25033 25779 25250 1032407 78266618 3650637 73538382 6.041191149974054" general_stats: asserts: has_text: @@ -60,8 +60,8 @@ n: 4 star: asserts: - has_text: - text: "GSM461177 1032407.0 71.0 854812.0 82.8 70.65 102763.0 102412.0 102040.0 679.0 20.0 24.0 0.54 0.0 1.56 0.0 1.43 82072.0 7.95 32881.0 3.18 0.0 5.9 0.17 0 60888 1754" + has_text_matching: + expression: "GSM461177 1032407.0 71.0 854812.0 82.8 70.65 10276[23].0 102412.0 1020[34][0-9].0 679.0 20.0 24.0 0.54 0.0 1.56 0.0 1.43 82072.0 7.95 32881.0 3.18 0.0 5.9 0.17 0 60888 1754" MultiQC webpage: asserts: - that: "has_text" @@ -105,4 +105,4 @@ GSM461177: asserts: has_text: - text: "FBgn0031217 CG11377 chr2L + 102380 104142 1.003790 31.826454 55.206604" + text: "FBgn0031217\tCG11377\tchr2L\t+\t102380\t104142\t1.955939\t32.891647\t57.313370" From c159c3dee0e1609db9b42f000a68134a302b00ec Mon Sep 17 00:00:00 2001 From: Lucille Delisle Date: Fri, 15 Sep 2023 11:31:51 +0200 Subject: [PATCH 22/22] Language editing Co-authored-by: Marius van den Beek --- workflows/transcriptomics/rnaseq-pe/CHANGELOG.md | 8 ++++---- workflows/transcriptomics/rnaseq-pe/README.md | 10 +++++----- .../rnaseq-pe/rnaseq-pe-tests.yml | 2 +- workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga | 16 ++++++++-------- workflows/transcriptomics/rnaseq-sr/CHANGELOG.md | 8 ++++---- workflows/transcriptomics/rnaseq-sr/README.md | 10 +++++----- .../rnaseq-sr/rnaseq-sr-tests.yml | 2 +- workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga | 16 ++++++++-------- 8 files changed, 36 insertions(+), 36 deletions(-) diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md index da2633651..e1eee3d27 100644 --- a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md @@ -1,14 +1,14 @@ # Changelog -## [0.5] 2023-03-17 +## [0.5] 2023-09-15 ### Automatic update - `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` ### Manual update -- Use STAR to compute normalized strand splitted coverage -- Propose StringTie to compute FPKM etc... -- Put cufflinks step optional +- Use STAR to compute normalized strand-specific coverage +- Add an option to use StringTie to compute FPKM +- Make cufflinks step optional ## [0.4.1] 2023-09-14 - add author in dockstore file diff --git a/workflows/transcriptomics/rnaseq-pe/README.md b/workflows/transcriptomics/rnaseq-pe/README.md index bfffd01fc..3640d4976 100644 --- a/workflows/transcriptomics/rnaseq-pe/README.md +++ b/workflows/transcriptomics/rnaseq-pe/README.md @@ -17,24 +17,24 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM - 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 -- strandness: For stranded RNA, reverse means that the first read in pair is complementary to the coding sequence, forward means that the first read in pair is in the same orientation as the coding sequence. This will help you to get from STAR only the counts corresponding to your library preparation. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. +- 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. ## 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 stranded specific normalized coverage (on uniquely mapped reads). -- A multiQC is run to have an overview of the QC. This can also be used to get the strandness. +- 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). +- 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. - The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1). -- Coverage unstranded is computed with bedtools and normalized to the number of million uniquely mapped reads. +- Unstranded coverage is computed with bedtools and normalized to the number of million uniquely mapped reads. - The three coverage files are converted to bigwig. ### Warning -- The coverage stranded output depends on the strandness of the library: +- The coverage stranded output depends on the strandedness of the library: - If you have an unstranded library, stranded coverages are useless - If you have a forward stranded library, the label matches the orientation of the first read in pairs. - If you have a reverse stranded library, the label matches the orientation of the second read in pairs. diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml index 3e43a8bb9..f9a976c04 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe-tests.yml @@ -23,7 +23,7 @@ forward_adapter: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC reverse_adapter: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT reference_genome: dm6 - strandness: unstranded + strandedness: unstranded cufflinks_FPKM: false stringtie_FPKM: true outputs: diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga index 3b7deb7c5..3545eec5b 100644 --- a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga +++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga @@ -157,10 +157,10 @@ "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": "strandness" + "name": "strandedness" } ], - "label": "strandness", + "label": "strandedness", "name": "Input parameter", "outputs": [], "position": { @@ -470,7 +470,7 @@ } }, "inputs": [], - "label": "Get Stringtie strandness parameter", + "label": "Get Stringtie strandedness parameter", "name": "Map parameter value", "outputs": [ { @@ -1047,7 +1047,7 @@ "input_subworkflow_step_id": 2, "output_name": "signal_unique_str2" }, - "strandness": { + "strandedness": { "id": 5, "input_subworkflow_step_id": 0, "output_name": "output" @@ -1084,10 +1084,10 @@ "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": "strandness" + "name": "strandedness" } ], - "label": "strandness", + "label": "strandedness", "name": "Input parameter", "outputs": [], "position": { @@ -1758,7 +1758,7 @@ "id": 14, "output_name": "mapped_reads" }, - "rna_strandness": { + "rna_strandedness": { "id": 13, "output_name": "output_param_text" }, @@ -1803,7 +1803,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": 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_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandedness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1+galaxy1", "type": "tool", "uuid": "4c7d6852-faac-4269-a7fa-92f93ebdab4c", diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md index 37e65fb84..90f092bac 100644 --- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md +++ b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md @@ -1,14 +1,14 @@ # Changelog -## [0.5] 2023-03-17 +## [0.5] 2023-09-15 ### Automatic update - `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` ### Manual update -- Use STAR to compute normalized strand splitted coverage -- Propose StringTie to compute FPKM etc... -- Put cufflinks step optional +- Use STAR to compute normalized strand-specific coverage +- Add an option to use StringTie to compute FPKM +- Make cufflinks step optional ## [0.4.1] 2023-09-14 - add author in dockstore file diff --git a/workflows/transcriptomics/rnaseq-sr/README.md b/workflows/transcriptomics/rnaseq-sr/README.md index 7a7cc1064..09236c628 100644 --- a/workflows/transcriptomics/rnaseq-sr/README.md +++ b/workflows/transcriptomics/rnaseq-sr/README.md @@ -17,24 +17,24 @@ chrM chrM_gene exon 0 16299 . - . gene_id "chrM_gene_minus"; transcript_id "chrM - forward adapter sequence: 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 -- strandness: 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. This will help you to get from STAR only the counts corresponding to your library preparation. This is also used for the stranded coverage and for FPKM computation with cufflinks/StringTie. +- strandedness: 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. 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. ## 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 stranded specific normalized coverage (on uniquely mapped reads). -- A multiQC is run to have an overview of the QC. This can also be used to get the strandness. +- 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). +- 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 (this step is optional). - The BAM is filtered to keep only uniquely mapped reads (tag NH:i:1). -- Coverage unstranded is computed with bedtools and normalized to the number of million uniquely mapped reads. +- Unstranded coverage is computed with bedtools and normalized to the number of million uniquely mapped reads. - The three coverage files are converted to bigwig. ### Warning -- The coverage stranded output depends on the strandness of the library: +- The coverage stranded output depends on the strandedness of the library: - If you have an unstranded library, stranded coverages are useless - If you have a forward stranded library, the label matches the orientation of reads. - If you have a reverse stranded library, `forward` should correspond to genes on the forward strand and uses the reads mapped on the reverse strand. `reverse` should correspond to genes on the reverse strand and uses the reads mapped on the forward strand. diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml index 437281102..23645d313 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr-tests.yml @@ -13,7 +13,7 @@ location: https://zenodo.org/record/4541751/files/GSM461177_1_subsampled.fastqsanger forward_adapter: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC reference_genome: dm6 - strandness: unstranded + strandedness: unstranded cufflinks_FPKM: true stringtie_FPKM: true outputs: diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga index d34262c4c..95fe5e1bd 100644 --- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga +++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga @@ -130,10 +130,10 @@ "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": "strandness" + "name": "strandedness" } ], - "label": "strandness", + "label": "strandedness", "name": "Input parameter", "outputs": [], "position": { @@ -444,7 +444,7 @@ } }, "inputs": [], - "label": "Get Stringtie strandness parameter", + "label": "Get Stringtie strandedness parameter", "name": "Map parameter value", "outputs": [ { @@ -1026,7 +1026,7 @@ "input_subworkflow_step_id": 2, "output_name": "signal_unique_str2" }, - "strandness": { + "strandedness": { "id": 4, "input_subworkflow_step_id": 0, "output_name": "output" @@ -1063,10 +1063,10 @@ "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": "strandness" + "name": "strandedness" } ], - "label": "strandness", + "label": "strandedness", "name": "Input parameter", "outputs": [], "position": { @@ -1737,7 +1737,7 @@ "id": 13, "output_name": "mapped_reads" }, - "rna_strandness": { + "rna_strandedness": { "id": 12, "output_name": "output_param_text" }, @@ -1782,7 +1782,7 @@ "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": 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_state": "{\"__job_resource\": {\"__job_resource__select\": \"no\", \"__current_case__\": 0}, \"adv\": {\"abundance_estimation\": true, \"omit_sequences\": \"\", \"name_prefix\": null, \"fraction\": \"0.01\", \"min_tlen\": \"200\", \"min_anchor_len\": \"10\", \"min_anchor_cov\": \"1\", \"min_bundle_cov\": \"1\", \"bdist\": \"50\", \"bundle_fraction\": \"1.0\", \"disable_trimming\": false, \"multi_mapping\": false, \"point_features\": {\"__class__\": \"RuntimeValue\"}}, \"guide\": {\"use_guide\": \"yes\", \"__current_case__\": 1, \"guide_source\": {\"guide_gff_select\": \"history\", \"__current_case__\": 1, \"ref_hist\": {\"__class__\": \"ConnectedValue\"}}, \"input_estimation\": true, \"special_outputs\": {\"special_outputs_select\": \"no\", \"__current_case__\": 2}, \"coverage_file\": false}, \"input_options\": {\"input_mode\": \"short_reads\", \"__current_case__\": 0, \"input_bam\": {\"__class__\": \"ConnectedValue\"}}, \"rna_strandedness\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", "tool_version": "2.2.1+galaxy1", "type": "tool", "uuid": "4c7d6852-faac-4269-a7fa-92f93ebdab4c",