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Upgrade scRNA-seq workflows from 0.4 to 0.5 #536

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merged 4 commits into from
Sep 25, 2024
Merged

Upgrade scRNA-seq workflows from 0.4 to 0.5 #536

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cbb709d
upgrade tools
lldelisle Sep 25, 2024
5d18e26
fix test syntax
lldelisle Sep 25, 2024
6902cef
update changelog and versions
lldelisle Sep 25, 2024
e43a906
fix tests for new multiQC
lldelisle Sep 25, 2024
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6 changes: 6 additions & 0 deletions workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,11 @@
# Changelog

## [0.5] 2024-09-25

### Manual update
- `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1`
- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0`

## [0.4] 2024-04-08

### Automatic update
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16 changes: 5 additions & 11 deletions workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
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Expand Up @@ -54,15 +54,11 @@
Number of expected cells: 500
outputs:
MultiQC_STARsolo:
class: File
asserts:
- that: "has_text_matching"
expression: ">subsample</th><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped_percent \"><div class=\"wrapper\"><span class=\"bar\""
- that: "has_text_matching"
expression: "></span><span class=\"val\">3[0-9].[0-9]%</span></div></td><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped \"><div class=\"wrapper\"><span class=\"bar\""
has_text_matching:
expression: "<td class=\"data-coloured mqc_generalstats_star_uniquely_mapped_percent_1 \"><div class=\"wrapper\"><span class=\"bar\"></span><span class=\"val\">33.[0-9]<span class=\"mqc_small_space\"></span>%</span></div></td>"
Seurat input for gene expression (filtered):
class: Collection
collection_type: list:list
attributes: { collection_type: list:list }
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element_tests:
subsample:
elements:
Expand All @@ -79,8 +75,7 @@
has_line:
line: "FBgn0250732 gfzf"
CITE-seq-Count report:
class: Collection
collection_type: list
attributes: { collection_type: list }
element_tests:
subsample:
asserts:
Expand All @@ -93,8 +88,7 @@
- that: "has_line"
line: "Percentage unmapped: 1"
Seurat input for CMO (UMI):
class: Collection
collection_type: list:list
attributes: { collection_type: list:list }
element_tests:
subsample:
elements:
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55 changes: 28 additions & 27 deletions workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
{
"a_galaxy_workflow": "true",
"annotation": "This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.",
"comments": [],
"creator": [
{
"class": "Person",
Expand Down Expand Up @@ -30,7 +31,7 @@
],
"format-version": "0.1",
"license": "MIT",
"release": "0.4",
"release": "0.5",
"name": "scRNA-seq_preprocessing_10X_cellPlex",
"steps": {
"0": {
Expand Down Expand Up @@ -464,7 +465,7 @@
},
"5": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
"errors": null,
"id": 5,
"input_connections": {
Expand Down Expand Up @@ -572,23 +573,23 @@
"output_name": "reads_per_gene"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy0",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
"tool_shed_repository": {
"changeset_revision": "42ce70172b72",
"changeset_revision": "45795f582ae9",
"name": "rna_starsolo",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.7.11a+galaxy0",
"tool_state": "{\"outWig\": {\"outWigType\": \"None\", \"__current_case__\": 0, \"outWigStrand\": \"false\"}, \"refGenomeSource\": {\"geneSource\": \"indexed\", \"__current_case__\": 0, \"GTFconditional\": {\"GTFselect\": \"without-gtf-with-gtf\", \"__current_case__\": 1, \"genomeDir\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfile\": {\"__class__\": \"ConnectedValue\"}, \"sjdbGTFfeatureExon\": \"exon\", \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"ConnectedValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"ConnectedValue\"}, \"params\": {\"chemistry\": \"Cv3\", \"__current_case__\": 1}, \"soloBarcodeReadLength\": {\"__class__\": \"ConnectedValue\"}, \"umidedup\": {\"soloUMIdedup\": \"1MM_CR\", \"__current_case__\": 4, \"soloUMIfiltering\": \"-\"}, \"soloCBmatchWLtype\": \"1MM_multi\"}, \"solo\": {\"soloStrand\": \"Forward\", \"soloFeatures\": \"Gene\", \"wasp_conditional\": {\"waspOutputMode\": \"\", \"__current_case__\": 1}, \"filter\": {\"filter_type\": \"no_filter\", \"__current_case__\": 3, \"output_raw\": \"true\"}, \"soloOutFormatFeaturesGeneField3\": \"Gene Expression\", \"outSAMattributes\": [\"NH\", \"HI\", \"AS\", \"nM\", \"GX\", \"GN\", \"CB\", \"UB\"], \"quantModeGene\": true, \"outSAMunmapped\": false, \"outSAMmapqUnique\": \"60\", \"junction_limits\": {\"limitOutSJoneRead\": \"1000\", \"limitOutSJcollapsed\": \"1000000\", \"limitSjdbInsertNsj\": \"1000000\"}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "2.7.11a+galaxy1",
"type": "tool",
"uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5",
"when": null,
"workflow_outputs": []
},
"6": {
"annotation": "",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"errors": null,
"id": 6,
"input_connections": {
Expand All @@ -605,13 +606,13 @@
"label": "multiQC",
"name": "MultiQC",
"outputs": [
{
"name": "stats",
"type": "input"
},
{
"name": "html_report",
"type": "html"
},
{
"name": "stats",
"type": "tabular"
}
],
"position": {
Expand All @@ -625,15 +626,15 @@
"output_name": "stats"
}
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1",
"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
"tool_shed_repository": {
"changeset_revision": "abfd8a6544d7",
"changeset_revision": "f7e2f1eb3a16",
"name": "multiqc",
"owner": "iuc",
"tool_shed": "toolshed.g2.bx.psu.edu"
},
"tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"star\", \"__current_case__\": 28, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"log\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"type\": {\"type\": \"genecounts\", \"__current_case__\": 1, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.11+galaxy1",
"tool_version": "1.24.1+galaxy0",
"type": "tool",
"uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973",
"when": null,
Expand Down Expand Up @@ -954,7 +955,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -999,7 +1000,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1044,7 +1045,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1295,8 +1296,8 @@
]
}
},
"tags": "",
"uuid": "89502a02-ec65-400c-b428-68eda7ea6b40"
"tags": [],
"uuid": "933626df-33e9-46ac-8206-d297a7fcb83a"
},
"tool_id": null,
"type": "subworkflow",
Expand All @@ -1311,7 +1312,7 @@
]
}
},
"tags": "",
"tags": [],
"uuid": "a999ad68-faa9-4ccb-81b4-ac648af028bd"
},
"tool_id": null,
Expand Down Expand Up @@ -1534,7 +1535,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1753,7 +1754,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1798,7 +1799,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -1843,7 +1844,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1",
"tool_shed_repository": {
"changeset_revision": "fbf99087e067",
"changeset_revision": "86755160afbf",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
Expand Down Expand Up @@ -2094,7 +2095,7 @@
]
}
},
"tags": "",
"tags": [],
"uuid": "79342c4e-bb7a-4b25-a214-7d5a10fbfd79"
},
"tool_id": null,
Expand Down Expand Up @@ -2166,6 +2167,6 @@
"tags": [
"#single-cell"
],
"uuid": "b8bd25f7-caa3-44da-8329-26dce6d46636",
"version": 4
"uuid": "470536e7-ac58-4859-94d6-2085be9c2e17",
"version": 3
}
10 changes: 3 additions & 7 deletions workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,15 +29,11 @@
filetype: tabular
outputs:
'MultiQC on input dataset(s): Webpage':
class: File
asserts:
- that: "has_text_matching"
expression: ">subsample</th><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped_percent \"><div class=\"wrapper\"><span class=\"bar\""
- that: "has_text_matching"
expression: "></span><span class=\"val\">3[0-9].[0-9]%</span></div></td><td class=\"data-coloured mqc-generalstats-star-uniquely_mapped \"><div class=\"wrapper\"><span class=\"bar\""
has_text_matching:
expression: "<td class=\"data-coloured mqc_generalstats_star_uniquely_mapped_percent_1 \"><div class=\"wrapper\"><span class=\"bar\"></span><span class=\"val\">33.[0-9]<span class=\"mqc_small_space\"></span>%</span></div></td>"
Seurat input for gene expression (filtered):
class: Collection
collection_type: list:list
attributes: { collection_type: list:list }
element_tests:
subsample:
elements:
Expand Down
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