diff --git a/workflows/scrna-seq/fastq-to-matrix-10x/.dockstore.yml b/workflows/scrna-seq/fastq-to-matrix-10x/.dockstore.yml
new file mode 100644
index 000000000..a092de320
--- /dev/null
+++ b/workflows/scrna-seq/fastq-to-matrix-10x/.dockstore.yml
@@ -0,0 +1,36 @@
+version: 1.2
+workflows:
+- name: scrna-seq-fastq-to-matrix-10x-cellplex
+ subclass: Galaxy
+ publish: true
+ primaryDescriptorPath: /scrna-seq-fastq-to-matrix-10x-cellplex.ga
+ testParameterFiles:
+ - /scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
+ authors:
+ - name: Lucille Delisle
+ orcid: 0000-0002-1964-4960
+ - name: Mehmet Tekman
+ orcid: 0000-0002-4181-2676
+ - name: Hans-Rudolf Hotz
+ orcid: 0000-0002-2799-424X
+ - name: Daniel Blankenberg
+ orcid: 0000-0002-6833-9049
+ - name: Wendi Bacon
+ orcid: 0000-0002-8170-8806
+- name: scrna-seq-fastq-to-matrix-10x-v3
+ subclass: Galaxy
+ publish: true
+ primaryDescriptorPath: /scrna-seq-fastq-to-matrix-10x-v3.ga
+ testParameterFiles:
+ - /scrna-seq-fastq-to-matrix-10x-v3-tests.yml
+ authors:
+ - name: Lucille Delisle
+ orcid: 0000-0002-1964-4960
+ - name: Mehmet Tekman
+ orcid: 0000-0002-4181-2676
+ - name: Hans-Rudolf Hotz
+ orcid: 0000-0002-2799-424X
+ - name: Daniel Blankenberg
+ orcid: 0000-0002-6833-9049
+ - name: Wendi Bacon
+ orcid: 0000-0002-8170-8806
diff --git a/workflows/scrna-seq/fastq-to-matrix-10x/CHANGELOG.md b/workflows/scrna-seq/fastq-to-matrix-10x/CHANGELOG.md
new file mode 100644
index 000000000..2b101bc0a
--- /dev/null
+++ b/workflows/scrna-seq/fastq-to-matrix-10x/CHANGELOG.md
@@ -0,0 +1,5 @@
+# Changelog
+
+## [0.1] 2023-12-01
+
+First release.
diff --git a/workflows/scrna-seq/fastq-to-matrix-10x/README.md b/workflows/scrna-seq/fastq-to-matrix-10x/README.md
new file mode 100644
index 000000000..7afb0b453
--- /dev/null
+++ b/workflows/scrna-seq/fastq-to-matrix-10x/README.md
@@ -0,0 +1,3 @@
+# Single-cell RNA-seq fastq to matrix for 10X data
+
+TODO
diff --git a/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
new file mode 100644
index 000000000..8b21b4843
--- /dev/null
+++ b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
@@ -0,0 +1,117 @@
+- doc: Test outline for scrna-seq-fastq-to-matrix-10X-cellplex.ga
+ job:
+ fastq PE collection GEX:
+ class: Collection
+ collection_type: list:paired
+ elements:
+ - class: Collection
+ type: paired
+ identifier: subsample
+ elements:
+ - identifier: forward
+ class: File
+ location: https://zenodo.org/records/10229382/files/subSample_GEX_R1.fastq.gz
+ filetype: fastqsanger.gz
+ - identifier: reverse
+ class: File
+ location: https://zenodo.org/records/10229382/files/subSample_GEX_R2.fastq.gz
+ filetype: fastqsanger.gz
+ reference genome: mm10full # To test on usegalaxy.eu
+ gtf:
+ class: File
+ location: https://zenodo.org/records/10079673/files/mm10_custom102_allGastruloids_min10_extended.gtf.gz
+ decompress: true
+ filetype: gtf
+ cellranger_barcodes_3M-february-2018.txt:
+ class: File
+ path: https://zenodo.org/record/3457880/files/3M-february-2018.txt.gz
+ decompress: true
+ filetype: tabular
+ fastq PE collection CMO:
+ class: Collection
+ collection_type: list:paired
+ elements:
+ - class: Collection
+ type: paired
+ identifier: subsample
+ elements:
+ - identifier: forward
+ class: File
+ location: https://zenodo.org/records/10229382/files/subSample_CMO_R1.fastq.gz
+ filetype: fastqsanger.gz
+ - identifier: reverse
+ class: File
+ location: https://zenodo.org/records/10229382/files/subSample_CMO_R2.fastq.gz
+ filetype: fastqsanger.gz
+ sample name and CMO sequence collection:
+ class: Collection
+ collection_type: list
+ elements:
+ - class: File
+ identifier: subsample
+ location: https://zenodo.org/records/10229382/files/CMO.csv
+ filetype: csv
+ Number of expected cells (used by CITE-seq-Count)): 1000
+ outputs:
+ MultiQC_STARsolo:
+ class: File
+ asserts:
+ - that: "has_text_matching"
+ text: "7[0-9].[0-9]% | [0-9].[0-9] |
"
+ Seurat input for gene expression (filtered):
+ class: Collection
+ collection_type: list:list
+ elements:
+ class: Collection
+ collection_type: list
+ identifier: subsample
+ elements:
+ - class: File
+ identifier: matrix
+ asserts:
+ - has_line:
+ line: "55141 353 1026324"
+ - class: File
+ identifier: barcodes
+ asserts:
+ - has_line:
+ line: "AAACGAAAGCATGCAG"
+ - class: File
+ identifier: genes
+ asserts:
+ - has_line:
+ line: "ENSMUSG00000102693 4933401J01Rik"
+ CITE-seq-Count report:
+ class: File
+ asserts:
+ - that: "has_line"
+ line: "CITE-seq-Count Version: 1.4.4"
+ - that: "has_line"
+ line: "Reads processed: 1171367"
+ - that: "has_line"
+ line: "Percentage mapped: 99"
+ - that: "has_line"
+ line: "Percentage unmapped: 1"
+ Seurat input for CMO (UMI):
+ class: Collection
+ collection_type: list:list
+ elements:
+ class: Collection
+ collection_type: list
+ identifier: subsample
+ elements:
+ - class: File
+ identifier: matrix
+ asserts:
+ - has_line:
+ line: "8 6794880 220553"
+ - class: File
+ identifier: barcodes
+ asserts:
+ - has_line:
+ line: "CGGGTCAAGGATGGAG"
+ - class: File
+ identifier: genes
+ asserts:
+ - has_line:
+ line: "mESC.rep1-CGCGATATGGTCGGA"
diff --git a/workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-scRNA-seq_preprocessing_10X_cellPlex.ga b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
similarity index 82%
rename from workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-scRNA-seq_preprocessing_10X_cellPlex.ga
rename to workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
index ef55156b4..7937afd72 100644
--- a/workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-scRNA-seq_preprocessing_10X_cellPlex.ga
+++ b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga
@@ -30,6 +30,7 @@
],
"format-version": "0.1",
"license": "MIT",
+ "release": "0.1",
"name": "scRNA-seq_preprocessing_10X_cellPlex",
"steps": {
"0": {
@@ -48,20 +49,15 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 35.78334045410156,
- "height": 82.20001220703125,
- "left": 454.1499938964844,
- "right": 654.1499938964844,
- "top": -46.41667175292969,
- "width": 200,
- "x": 454.1499938964844,
- "y": -46.41667175292969
+ "left": 0,
+ "top": 0
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "eea58879-4368-4edf-ad0a-2dbd91de2db7",
+ "when": null,
"workflow_outputs": []
},
"1": {
@@ -80,20 +76,15 @@
"name": "Input parameter",
"outputs": [],
"position": {
- "bottom": 134.10000610351562,
- "height": 82.20001220703125,
- "left": 497.33331298828125,
- "right": 697.3333129882812,
- "top": 51.899993896484375,
- "width": 200,
- "x": 497.33331298828125,
- "y": 51.899993896484375
+ "left": 43.183319091796875,
+ "top": 98.31666564941406
},
"tool_id": null,
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "32f09d94-82fe-4c79-b86a-3af89fdb3088",
+ "when": null,
"workflow_outputs": []
},
"2": {
@@ -112,20 +103,15 @@
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 219.1666717529297,
- "height": 61.80000305175781,
- "left": 539.0999755859375,
- "right": 739.0999755859375,
- "top": 157.36666870117188,
- "width": 200,
- "x": 539.0999755859375,
- "y": 157.36666870117188
+ "left": 84.94998168945312,
+ "top": 203.78334045410156
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "8724cc04-fa9f-48df-ba31-6c47a03c9bde",
+ "when": null,
"workflow_outputs": []
},
"3": {
@@ -144,20 +130,15 @@
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 344.5,
- "height": 102.60000610351562,
- "left": 584.1500244140625,
- "right": 784.1500244140625,
- "top": 241.89999389648438,
- "width": 200,
- "x": 584.1500244140625,
- "y": 241.89999389648438
+ "left": 130.00003051757812,
+ "top": 288.31666564941406
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "bc4574f1-2a6f-44db-bed3-6d066d5ce42f",
+ "when": null,
"workflow_outputs": []
},
"4": {
@@ -176,20 +157,15 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 473.1999969482422,
- "height": 82.19999694824219,
- "left": 641.8333129882812,
- "right": 841.8333129882812,
- "top": 391,
- "width": 200,
- "x": 641.8333129882812,
- "y": 391
+ "left": 187.68331909179688,
+ "top": 437.4166717529297
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "4a52f2cf-ee11-47ac-9f24-ce5e49b8434e",
+ "when": null,
"workflow_outputs": []
},
"5": {
@@ -208,20 +184,15 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 573.1999969482422,
- "height": 82.19999694824219,
- "left": 668.8333129882812,
- "right": 868.8333129882812,
- "top": 491,
- "width": 200,
- "x": 668.8333129882812,
- "y": 491
+ "left": 214.68331909179688,
+ "top": 537.4166717529297
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"format\": [\"csv\"], \"tag\": \"\", \"collection_type\": \"list\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "dce97235-a4ba-4bfd-9d1f-60d3942f624b",
+ "when": null,
"workflow_outputs": []
},
"6": {
@@ -240,20 +211,15 @@
"name": "Input parameter",
"outputs": [],
"position": {
- "bottom": 746.4333190917969,
- "height": 143.39999389648438,
- "left": 710.36669921875,
- "right": 910.36669921875,
- "top": 603.0333251953125,
- "width": 200,
- "x": 710.36669921875,
- "y": 603.0333251953125
+ "left": 256.2167053222656,
+ "top": 649.4499969482422
},
"tool_id": null,
"tool_state": "{\"parameter_type\": \"integer\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "5ca25d6a-112f-4870-b5a4-163a055360c0",
+ "when": null,
"workflow_outputs": []
},
"7": {
@@ -291,14 +257,8 @@
"name": "scRNA-seq_preprocessing_10X_v3_Bundle",
"outputs": [],
"position": {
- "bottom": 321.6000061035156,
- "height": 255.60000610351562,
- "left": 1062.933349609375,
- "right": 1262.933349609375,
- "top": 66,
- "width": 200,
- "x": 1062.933349609375,
- "y": 66
+ "left": 608.7833557128906,
+ "top": 112.41667175292969
},
"subworkflow": {
"a_galaxy_workflow": "true",
@@ -350,20 +310,15 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 265.1999969482422,
- "height": 82.19999694824219,
- "left": 541.0499877929688,
- "right": 741.0499877929688,
- "top": 183,
- "width": 200,
- "x": 541.0499877929688,
- "y": 183
+ "left": 0.0,
+ "top": 0
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "eea58879-4368-4edf-ad0a-2dbd91de2db7",
+ "when": null,
"workflow_outputs": []
},
"1": {
@@ -382,20 +337,15 @@
"name": "Input parameter",
"outputs": [],
"position": {
- "bottom": 375.1999969482422,
- "height": 82.19999694824219,
- "left": 579,
- "right": 779,
- "top": 293,
- "width": 200,
- "x": 579,
- "y": 293
+ "left": 37.95001220703125,
+ "top": 110
},
"tool_id": null,
"tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
"type": "parameter_input",
"uuid": "adf0f555-5974-44b9-a067-37e4054cd662",
+ "when": null,
"workflow_outputs": []
},
"2": {
@@ -414,20 +364,15 @@
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 447.8000030517578,
- "height": 61.80000305175781,
- "left": 641.066650390625,
- "right": 841.066650390625,
- "top": 386,
- "width": 200,
- "x": 641.066650390625,
- "y": 386
+ "left": 100.01666259765625,
+ "top": 203
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "8724cc04-fa9f-48df-ba31-6c47a03c9bde",
+ "when": null,
"workflow_outputs": []
},
"3": {
@@ -446,20 +391,15 @@
"name": "Input dataset",
"outputs": [],
"position": {
- "bottom": 584.6000061035156,
- "height": 102.60000610351562,
- "left": 715.0333251953125,
- "right": 915.0333251953125,
- "top": 482,
- "width": 200,
- "x": 715.0333251953125,
- "y": 482
+ "left": 173.98333740234375,
+ "top": 299
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
"type": "data_input",
"uuid": "bc4574f1-2a6f-44db-bed3-6d066d5ce42f",
+ "when": null,
"workflow_outputs": []
},
"4": {
@@ -519,14 +459,8 @@
}
],
"position": {
- "bottom": 1215.4000244140625,
- "height": 652.4000244140625,
- "left": 1088.800048828125,
- "right": 1288.800048828125,
- "top": 563,
- "width": 200,
- "x": 1088.800048828125,
- "y": 563
+ "left": 547.7500610351562,
+ "top": 380
},
"post_job_actions": {
"HideDatasetActionoutput_BAM": {
@@ -572,10 +506,11 @@
"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\"}, \"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\": \"true\", \"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_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\"}, \"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\": true, \"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": "2.7.10b+galaxy3",
"type": "tool",
"uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5",
+ "when": null,
"workflow_outputs": []
},
"5": {
@@ -607,14 +542,8 @@
}
],
"position": {
- "bottom": 791.5833282470703,
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- "left": 1368.066650390625,
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- "top": 555.9833374023438,
- "width": 200,
- "x": 1368.066650390625,
- "y": 555.9833374023438
+ "left": 827.0166625976562,
+ "top": 372.98333740234375
},
"post_job_actions": {
"HideDatasetActionstats": {
@@ -630,10 +559,11 @@
"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_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",
"type": "tool",
"uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973",
+ "when": null,
"workflow_outputs": [
{
"label": "MultiQC on input dataset(s): Webpage",
@@ -687,14 +617,8 @@
}
],
"position": {
- "bottom": 1264.3833312988281,
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- "top": 829.9833374023438,
- "width": 200,
- "x": 1368.066650390625,
- "y": 829.9833374023438
+ "left": 827.0166625976562,
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"post_job_actions": {
"HideDatasetActionbarcodes_out": {
@@ -734,6 +658,7 @@
"tool_version": "1.10.0+galaxy2",
"type": "tool",
"uuid": "2ba61d0f-82ae-4044-a7ad-41df1cf8c9b6",
+ "when": null,
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+ "changeset_revision": "ddf54b12c295",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1968,6 +1772,7 @@
"tool_version": "1.1.2",
"type": "tool",
"uuid": "ac2f7a73-a742-4977-b902-aba871059cb6",
+ "when": null,
"workflow_outputs": []
},
"7": {
@@ -2004,14 +1809,8 @@
}
],
"position": {
- "bottom": 474.3999938964844,
- "height": 164.39999389648438,
- "left": 179,
- "right": 379,
- "top": 310,
- "width": 200,
- "x": 179,
- "y": 310
+ "left": 829,
+ "top": 58
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -2021,10 +1820,11 @@
}
},
"tool_id": "__RELABEL_FROM_FILE__",
- "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"RuntimeValue\"}, \"strict\": \"false\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"RuntimeValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "d627ba62-eeb9-49a3-b46f-120dd8c8e3d8",
+ "when": null,
"workflow_outputs": []
},
"8": {
@@ -2052,14 +1852,8 @@
}
],
"position": {
- "bottom": 629.3999938964844,
- "height": 164.39999389648438,
- "left": 177,
- "right": 377,
- "top": 465,
- "width": 200,
- "x": 177,
- "y": 465
+ "left": 827,
+ "top": 213
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -2069,10 +1863,11 @@
}
},
"tool_id": "__RELABEL_FROM_FILE__",
- "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "e4fad6a7-30e3-4b66-a9bd-5f11f7ea18db",
+ "when": null,
"workflow_outputs": []
},
"9": {
@@ -2100,14 +1895,8 @@
}
],
"position": {
- "bottom": 780.3999938964844,
- "height": 164.39999389648438,
- "left": 173,
- "right": 373,
- "top": 616,
- "width": 200,
- "x": 173,
- "y": 616
+ "left": 823,
+ "top": 364
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -2117,10 +1906,11 @@
}
},
"tool_id": "__RELABEL_FROM_FILE__",
- "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "fe80aa41-a8e4-4000-af6b-6c9713de9006",
+ "when": null,
"workflow_outputs": []
},
"10": {
@@ -2152,14 +1942,8 @@
}
],
"position": {
- "bottom": 615.6000061035156,
- "height": 235.60000610351562,
- "left": 414,
- "right": 614,
- "top": 380,
- "width": 200,
- "x": 414,
- "y": 380
+ "left": 1064,
+ "top": 128
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -2173,6 +1957,7 @@
"tool_version": "1.0.0",
"type": "tool",
"uuid": "a494a5d5-d908-448e-a406-c7f78d81c10b",
+ "when": null,
"workflow_outputs": []
},
"11": {
@@ -2201,14 +1986,8 @@
}
],
"position": {
- "bottom": 493.6000061035156,
- "height": 113.60000610351562,
- "left": 634,
- "right": 834,
- "top": 380,
- "width": 200,
- "x": 634,
- "y": 380
+ "left": 1284,
+ "top": 128
},
"post_job_actions": {
"RenameDatasetActionoutput": {
@@ -2224,6 +2003,7 @@
"tool_version": "1.1.0",
"type": "tool",
"uuid": "95eb63d6-f1a2-4f0d-b426-fc46a5133471",
+ "when": null,
"workflow_outputs": [
{
"label": "STARsolo cell ranger-like output",
@@ -2236,9 +2016,10 @@
"tags": "",
"uuid": "600e9a1d-4fd3-4351-8427-4fbd215af136"
},
- "tool_id": "ff567bf77a6f7387",
+ "tool_id": null,
"type": "subworkflow",
"uuid": "1626e9ae-6466-4ab1-852b-e237a5d3b601",
+ "when": null,
"workflow_outputs": [
{
"label": "Seurat input for CMO (UMI)",
@@ -2268,14 +2049,8 @@
}
],
"position": {
- "bottom": 873.0166625976562,
- "height": 134,
- "left": 1854.8499755859375,
- "right": 2054.8499755859375,
- "top": 739.0166625976562,
- "width": 200,
- "x": 1854.8499755859375,
- "y": 739.0166625976562
+ "left": 1400.6999816894531,
+ "top": 785.4333343505859
},
"post_job_actions": {
"RenameDatasetActiondata_param": {
@@ -2291,6 +2066,7 @@
"tool_version": "0.1.0",
"type": "tool",
"uuid": "3e819040-a643-4aa7-949c-42becbf21edd",
+ "when": null,
"workflow_outputs": [
{
"label": "Renamed Seurat input for CMO (UMI)",
@@ -2303,6 +2079,6 @@
"tags": [
"scRNA-seq"
],
- "uuid": "9d855c38-7b44-45e7-a132-fd911864fa2c",
- "version": 20
+ "uuid": "f69bf194-9fbd-4285-8bdc-6c9702f97534",
+ "version": 2
}
\ No newline at end of file
diff --git a/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
new file mode 100644
index 000000000..18233ee1e
--- /dev/null
+++ b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
@@ -0,0 +1,58 @@
+- doc: Test outline for scrna-seq-fastq-to-matrix-10x-v3.ga
+ job:
+ fastq PE collection:
+ class: Collection
+ collection_type: list:paired
+ elements:
+ - class: Collection
+ type: paired
+ identifier: subsample
+ elements:
+ - identifier: forward
+ class: File
+ location: https://zenodo.org/records/10229382/files/subSample_GEX_R1.fastq.gz
+ filetype: fastqsanger.gz
+ - identifier: reverse
+ class: File
+ location: https://zenodo.org/records/10229382/files/subSample_GEX_R2.fastq.gz
+ filetype: fastqsanger.gz
+ reference genome: mm10full # To test on usegalaxy.eu
+ gtf:
+ class: File
+ location: https://zenodo.org/records/10079673/files/mm10_custom102_allGastruloids_min10_extended.gtf.gz
+ decompress: true
+ filetype: gtf
+ cellranger_barcodes_3M-february-2018.txt:
+ class: File
+ path: https://zenodo.org/record/3457880/files/3M-february-2018.txt.gz
+ decompress: true
+ filetype: tabular
+ outputs:
+ 'MultiQC on input dataset(s): Webpage':
+ class: File
+ asserts:
+ - that: "has_text_matching"
+ text: "7[0-9].[0-9]% | [0-9].[0-9] |
"
+ Seurat input for gene expression (filtered):
+ class: Collection
+ collection_type: list:list
+ elements:
+ class: Collection
+ collection_type: list
+ identifier: subsample
+ elements:
+ - class: File
+ identifier: matrix
+ asserts:
+ - has_line:
+ line: "55141 353 1026324"
+ - class: File
+ identifier: barcodes
+ asserts:
+ - has_line:
+ line: "AAACGAAAGCATGCAG"
+ - class: File
+ identifier: genes
+ asserts:
+ - has_line:
+ line: "ENSMUSG00000102693 4933401J01Rik"
diff --git a/workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-scRNA-seq_preprocessing_10X_v3_Bundle.ga b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
similarity index 77%
rename from workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-scRNA-seq_preprocessing_10X_v3_Bundle.ga
rename to workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
index 95d83c4f5..114b32f01 100644
--- a/workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-scRNA-seq_preprocessing_10X_v3_Bundle.ga
+++ b/workflows/scrna-seq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga
@@ -33,159 +33,133 @@
"name": "scRNA-seq_preprocessing_10X_v3_Bundle",
"steps": {
"0": {
- "annotation": "Available at https://zenodo.org/record/3457880/files/3M-february-2018.txt.gz",
+ "annotation": "Collection of Pairs with fastqs one item per sample",
"content_id": null,
"errors": null,
"id": 0,
"input_connections": {},
"inputs": [
{
- "description": "Available at https://zenodo.org/record/3457880/files/3M-february-2018.txt.gz",
- "name": "cellranger_barcodes_3M-february-2018.txt"
+ "description": "Collection of Pairs with fastqs one item per sample",
+ "name": "fastq PE collection"
}
],
- "label": "cellranger_barcodes_3M-february-2018.txt",
- "name": "Input dataset",
+ "label": "fastq PE collection",
+ "name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 80.60000610351562,
- "height": 102.60000610351562,
- "left": -276.9666748046875,
- "right": -76.9666748046875,
- "top": -22,
- "width": 200,
- "x": -276.9666748046875,
- "y": -22
+ "left": 0,
+ "top": 0
},
"tool_id": null,
- "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+ "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}",
"tool_version": null,
- "type": "data_input",
- "uuid": "bc4574f1-2a6f-44db-bed3-6d066d5ce42f",
+ "type": "data_collection_input",
+ "uuid": "eea58879-4368-4edf-ad0a-2dbd91de2db7",
+ "when": null,
"workflow_outputs": []
},
"1": {
- "annotation": "Gene annotations",
+ "annotation": "Choose your reference genome",
"content_id": null,
"errors": null,
"id": 1,
"input_connections": {},
"inputs": [
{
- "description": "Gene annotations",
- "name": "gtf"
+ "description": "Choose your reference genome",
+ "name": "reference genome"
}
],
- "label": "gtf",
- "name": "Input dataset",
+ "label": "reference genome",
+ "name": "Input parameter",
"outputs": [],
"position": {
- "bottom": -56.19999694824219,
- "height": 61.80000305175781,
- "left": -350.933349609375,
- "right": -150.933349609375,
- "top": -118,
- "width": 200,
- "x": -350.933349609375,
- "y": -118
+ "left": 37.95001220703125,
+ "top": 110
},
"tool_id": null,
- "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+ "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
"tool_version": null,
- "type": "data_input",
- "uuid": "8724cc04-fa9f-48df-ba31-6c47a03c9bde",
+ "type": "parameter_input",
+ "uuid": "adf0f555-5974-44b9-a067-37e4054cd662",
+ "when": null,
"workflow_outputs": []
},
"2": {
- "annotation": "Choose your reference genome",
+ "annotation": "Gene annotations",
"content_id": null,
"errors": null,
"id": 2,
"input_connections": {},
"inputs": [
{
- "description": "Choose your reference genome",
- "name": "reference genome"
+ "description": "Gene annotations",
+ "name": "gtf"
}
],
- "label": "reference genome",
- "name": "Input parameter",
+ "label": "gtf",
+ "name": "Input dataset",
"outputs": [],
"position": {
- "bottom": -128.8000030517578,
- "height": 82.19999694824219,
- "left": -413,
- "right": -213,
- "top": -211,
- "width": 200,
- "x": -413,
- "y": -211
+ "left": 100.01666259765625,
+ "top": 203
},
"tool_id": null,
- "tool_state": "{\"restrictOnConnections\": true, \"parameter_type\": \"text\", \"optional\": false}",
+ "tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
- "type": "parameter_input",
- "uuid": "adf0f555-5974-44b9-a067-37e4054cd662",
- "workflow_outputs": [
- {
- "label": null,
- "output_name": "output",
- "uuid": "fc570cab-0c28-4a07-bccf-35f2429681bd"
- }
- ]
+ "type": "data_input",
+ "uuid": "8724cc04-fa9f-48df-ba31-6c47a03c9bde",
+ "when": null,
+ "workflow_outputs": []
},
"3": {
- "annotation": "Collection of Pairs with fastqs one item per sample",
+ "annotation": "Available at https://zenodo.org/record/3457880/files/3M-february-2018.txt.gz",
"content_id": null,
"errors": null,
"id": 3,
"input_connections": {},
"inputs": [
{
- "description": "Collection of Pairs with fastqs one item per sample",
- "name": "fastq PE collection"
+ "description": "Available at https://zenodo.org/record/3457880/files/3M-february-2018.txt.gz",
+ "name": "cellranger_barcodes_3M-february-2018.txt"
}
],
- "label": "fastq PE collection",
- "name": "Input dataset collection",
+ "label": "cellranger_barcodes_3M-february-2018.txt",
+ "name": "Input dataset",
"outputs": [],
"position": {
- "bottom": -238.8000030517578,
- "height": 82.19999694824219,
- "left": -450.95001220703125,
- "right": -250.95001220703125,
- "top": -321,
- "width": 200,
- "x": -450.95001220703125,
- "y": -321
+ "left": 173.98333740234375,
+ "top": 299
},
"tool_id": null,
- "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}",
+ "tool_state": "{\"optional\": false, \"tag\": \"\"}",
"tool_version": null,
- "type": "data_collection_input",
- "uuid": "eea58879-4368-4edf-ad0a-2dbd91de2db7",
+ "type": "data_input",
+ "uuid": "bc4574f1-2a6f-44db-bed3-6d066d5ce42f",
+ "when": null,
"workflow_outputs": []
},
"4": {
"annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3",
+ "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy4",
"errors": null,
"id": 4,
"input_connections": {
"refGenomeSource|GTFconditional|genomeDir": {
- "id": 2,
+ "id": 1,
"output_name": "output"
},
"refGenomeSource|GTFconditional|sjdbGTFfile": {
- "id": 1,
+ "id": 2,
"output_name": "output"
},
"sc|input_types|input_collection": {
- "id": 3,
+ "id": 0,
"output_name": "output"
},
"sc|soloCBwhitelist": {
- "id": 0,
+ "id": 3,
"output_name": "output"
}
},
@@ -223,14 +197,8 @@
}
],
"position": {
- "bottom": 711.4000244140625,
- "height": 652.4000244140625,
- "left": 96.80000305175781,
- "right": 296.8000030517578,
- "top": 59,
- "width": 200,
- "x": 96.80000305175781,
- "y": 59
+ "left": 547.7500610351562,
+ "top": 380
},
"post_job_actions": {
"HideDatasetActionoutput_BAM": {
@@ -269,17 +237,18 @@
"output_name": "reads_per_gene"
}
},
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy3",
+ "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.10b+galaxy4",
"tool_shed_repository": {
- "changeset_revision": "13022c3d3076",
+ "changeset_revision": "5ef7ec16b04f",
"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\"}, \"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\": \"true\", \"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": "2.7.10b+galaxy3",
+ "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\": true, \"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": "2.7.10b+galaxy4",
"type": "tool",
"uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5",
+ "when": null,
"workflow_outputs": []
},
"5": {
@@ -311,14 +280,8 @@
}
],
"position": {
- "bottom": 287.5833282470703,
- "height": 235.59999084472656,
- "left": 376.066650390625,
- "right": 576.066650390625,
- "top": 51.98333740234375,
- "width": 200,
- "x": 376.066650390625,
- "y": 51.98333740234375
+ "left": 827.0166625976562,
+ "top": 372.98333740234375
},
"post_job_actions": {
"HideDatasetActionstats": {
@@ -334,15 +297,16 @@
"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_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",
"type": "tool",
"uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973",
+ "when": null,
"workflow_outputs": [
{
"label": "MultiQC on input dataset(s): Webpage",
"output_name": "html_report",
- "uuid": "ff2d2093-da23-4c07-8797-ac32c84b1cce"
+ "uuid": "eb55ba68-0473-4b09-87b9-007be3a86098"
}
]
},
@@ -391,14 +355,8 @@
}
],
"position": {
- "bottom": 760.3833312988281,
- "height": 434.3999938964844,
- "left": 376.066650390625,
- "right": 576.066650390625,
- "top": 325.98333740234375,
- "width": 200,
- "x": 376.066650390625,
- "y": 325.98333740234375
+ "left": 827.0166625976562,
+ "top": 646.9833374023438
},
"post_job_actions": {
"HideDatasetActionbarcodes_out": {
@@ -438,6 +396,7 @@
"tool_version": "1.10.0+galaxy2",
"type": "tool",
"uuid": "2ba61d0f-82ae-4044-a7ad-41df1cf8c9b6",
+ "when": null,
"workflow_outputs": []
},
"7": {
@@ -470,14 +429,8 @@
"name": "Re-organize-STAR-solo-output",
"outputs": [],
"position": {
- "bottom": 674.1999969482422,
- "height": 215.1999969482422,
- "left": 654.0333251953125,
- "right": 854.0333251953125,
- "top": 459,
- "width": 200,
- "x": 654.0333251953125,
- "y": 459
+ "left": 1104.9833374023438,
+ "top": 780
},
"subworkflow": {
"a_galaxy_workflow": "true",
@@ -509,20 +462,15 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 313.8000030517578,
- "height": 61.80000305175781,
- "left": -650,
- "right": -450,
- "top": 252,
- "width": 200,
- "x": -650,
- "y": 252
+ "left": 0,
+ "top": 0
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "3e312de3-0895-4b46-ac51-9c1c7e341194",
+ "when": null,
"workflow_outputs": []
},
"1": {
@@ -541,20 +489,15 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 460.1999969482422,
- "height": 82.19999694824219,
- "left": -627,
- "right": -427,
- "top": 378,
- "width": 200,
- "x": -627,
- "y": 378
+ "left": 23,
+ "top": 126
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "4f8d1d99-0adc-40a8-a53b-ce9c1c614aeb",
+ "when": null,
"workflow_outputs": []
},
"2": {
@@ -573,20 +516,15 @@
"name": "Input dataset collection",
"outputs": [],
"position": {
- "bottom": 583.1999969482422,
- "height": 82.19999694824219,
- "left": -566,
- "right": -366,
- "top": 501,
- "width": 200,
- "x": -566,
- "y": 501
+ "left": 84,
+ "top": 249
},
"tool_id": null,
"tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
"tool_version": null,
"type": "data_collection_input",
"uuid": "266958e3-aacf-4b7f-8f74-6cbcdd5db4c0",
+ "when": null,
"workflow_outputs": []
},
"3": {
@@ -610,14 +548,8 @@
}
],
"position": {
- "bottom": 803.6000061035156,
- "height": 113.60000610351562,
- "left": -313,
- "right": -113,
- "top": 690,
- "width": 200,
- "x": -313,
- "y": 690
+ "left": 337,
+ "top": 438
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -637,6 +569,7 @@
"tool_version": "0.0.2",
"type": "tool",
"uuid": "ff023a14-a401-4ede-8dfb-2187d2d8ad84",
+ "when": null,
"workflow_outputs": []
},
"4": {
@@ -665,14 +598,8 @@
}
],
"position": {
- "bottom": 408.1999969482422,
- "height": 93.19999694824219,
- "left": -71,
- "right": 129,
- "top": 315,
- "width": 200,
- "x": -71,
- "y": 315
+ "left": 579,
+ "top": 63
},
"post_job_actions": {
"HideDatasetActionoutfile": {
@@ -683,7 +610,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
"tool_shed_repository": {
- "changeset_revision": "d698c222f354",
+ "changeset_revision": "ddf54b12c295",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -692,6 +619,7 @@
"tool_version": "1.1.2",
"type": "tool",
"uuid": "e8eed7c4-a41f-4bf7-bf5d-b4ed5023f1b8",
+ "when": null,
"workflow_outputs": []
},
"5": {
@@ -720,14 +648,8 @@
}
],
"position": {
- "bottom": 550.1999969482422,
- "height": 93.19999694824219,
- "left": -66,
- "right": 134,
- "top": 457,
- "width": 200,
- "x": -66,
- "y": 457
+ "left": 584,
+ "top": 205
},
"post_job_actions": {
"HideDatasetActionoutfile": {
@@ -738,7 +660,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
"tool_shed_repository": {
- "changeset_revision": "d698c222f354",
+ "changeset_revision": "ddf54b12c295",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -747,6 +669,7 @@
"tool_version": "1.1.2",
"type": "tool",
"uuid": "de152d11-daaa-4c96-ada8-7917c17e9543",
+ "when": null,
"workflow_outputs": []
},
"6": {
@@ -770,14 +693,8 @@
}
],
"position": {
- "bottom": 728.1999969482422,
- "height": 93.19999694824219,
- "left": -69,
- "right": 131,
- "top": 635,
- "width": 200,
- "x": -69,
- "y": 635
+ "left": 581,
+ "top": 383
},
"post_job_actions": {
"HideDatasetActionoutfile": {
@@ -788,7 +705,7 @@
},
"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
"tool_shed_repository": {
- "changeset_revision": "d698c222f354",
+ "changeset_revision": "ddf54b12c295",
"name": "text_processing",
"owner": "bgruening",
"tool_shed": "toolshed.g2.bx.psu.edu"
@@ -797,6 +714,7 @@
"tool_version": "1.1.2",
"type": "tool",
"uuid": "ac2f7a73-a742-4977-b902-aba871059cb6",
+ "when": null,
"workflow_outputs": []
},
"7": {
@@ -833,14 +751,8 @@
}
],
"position": {
- "bottom": 474.3999938964844,
- "height": 164.39999389648438,
- "left": 179,
- "right": 379,
- "top": 310,
- "width": 200,
- "x": 179,
- "y": 310
+ "left": 829,
+ "top": 58
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -850,10 +762,11 @@
}
},
"tool_id": "__RELABEL_FROM_FILE__",
- "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"RuntimeValue\"}, \"strict\": \"false\"}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"RuntimeValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "d627ba62-eeb9-49a3-b46f-120dd8c8e3d8",
+ "when": null,
"workflow_outputs": []
},
"8": {
@@ -881,14 +794,8 @@
}
],
"position": {
- "bottom": 629.3999938964844,
- "height": 164.39999389648438,
- "left": 177,
- "right": 377,
- "top": 465,
- "width": 200,
- "x": 177,
- "y": 465
+ "left": 827,
+ "top": 213
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -898,10 +805,11 @@
}
},
"tool_id": "__RELABEL_FROM_FILE__",
- "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "e4fad6a7-30e3-4b66-a9bd-5f11f7ea18db",
+ "when": null,
"workflow_outputs": []
},
"9": {
@@ -929,14 +837,8 @@
}
],
"position": {
- "bottom": 780.3999938964844,
- "height": 164.39999389648438,
- "left": 173,
- "right": 373,
- "top": 616,
- "width": 200,
- "x": 173,
- "y": 616
+ "left": 823,
+ "top": 364
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -946,10 +848,11 @@
}
},
"tool_id": "__RELABEL_FROM_FILE__",
- "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": \"false\"}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+ "tool_state": "{\"how\": {\"how_select\": \"txt\", \"__current_case__\": 0, \"labels\": {\"__class__\": \"ConnectedValue\"}, \"strict\": false}, \"input\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
"tool_version": "1.0.0",
"type": "tool",
"uuid": "fe80aa41-a8e4-4000-af6b-6c9713de9006",
+ "when": null,
"workflow_outputs": []
},
"10": {
@@ -981,14 +884,8 @@
}
],
"position": {
- "bottom": 615.6000061035156,
- "height": 235.60000610351562,
- "left": 414,
- "right": 614,
- "top": 380,
- "width": 200,
- "x": 414,
- "y": 380
+ "left": 1064,
+ "top": 128
},
"post_job_actions": {
"HideDatasetActionoutput": {
@@ -1002,6 +899,7 @@
"tool_version": "1.0.0",
"type": "tool",
"uuid": "a494a5d5-d908-448e-a406-c7f78d81c10b",
+ "when": null,
"workflow_outputs": []
},
"11": {
@@ -1030,14 +928,8 @@
}
],
"position": {
- "bottom": 493.6000061035156,
- "height": 113.60000610351562,
- "left": 634,
- "right": 834,
- "top": 380,
- "width": 200,
- "x": 634,
- "y": 380
+ "left": 1284,
+ "top": 128
},
"post_job_actions": {
"RenameDatasetActionoutput": {
@@ -1053,6 +945,7 @@
"tool_version": "1.1.0",
"type": "tool",
"uuid": "95eb63d6-f1a2-4f0d-b426-fc46a5133471",
+ "when": null,
"workflow_outputs": [
{
"label": "STARsolo cell ranger-like output",
@@ -1065,66 +958,15 @@
"tags": "",
"uuid": "600e9a1d-4fd3-4351-8427-4fbd215af136"
},
- "tool_id": "8eb0c6561d0cf9ad",
+ "tool_id": null,
"type": "subworkflow",
"uuid": "697a68da-9cb9-469b-8102-30c3a3ee589f",
+ "when": null,
"workflow_outputs": [
{
"label": "Seurat input for gene expression (filtered)",
"output_name": "STARsolo cell ranger-like output",
- "uuid": "615d658b-4b1c-4eab-8f2f-68f570da7b8b"
- }
- ]
- },
- "8": {
- "annotation": "",
- "content_id": "pick_value",
- "errors": null,
- "id": 8,
- "input_connections": {
- "style_cond|type_cond|pick_from_0|value": {
- "id": 7,
- "output_name": "STARsolo cell ranger-like output"
- }
- },
- "inputs": [],
- "label": "Rename STAR-solo output",
- "name": "Pick parameter value",
- "outputs": [
- {
- "name": "data_param",
- "type": "data"
- }
- ],
- "position": {
- "bottom": 775.3999938964844,
- "height": 154.39999389648438,
- "left": 940.0499877929688,
- "right": 1140.0499877929688,
- "top": 621,
- "width": 200,
- "x": 940.0499877929688,
- "y": 621
- },
- "post_job_actions": {
- "RenameDatasetActiondata_param": {
- "action_arguments": {
- "newname": "Seurat input for gene expression (filtered)"
- },
- "action_type": "RenameDatasetAction",
- "output_name": "data_param"
- }
- },
- "tool_id": "pick_value",
- "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"RuntimeValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "0.1.0",
- "type": "tool",
- "uuid": "cf5fb8a3-b970-40d8-bced-3faa6571faf4",
- "workflow_outputs": [
- {
- "label": "Renamed Seurat input for gene expression (filtered)",
- "output_name": "data_param",
- "uuid": "9d594fc3-b7e7-4b11-8596-e5dd894cde37"
+ "uuid": "6cb072df-9e26-456b-ab4f-bc95345b02b4"
}
]
}
@@ -1132,6 +974,6 @@
"tags": [
"scRNA-seq"
],
- "uuid": "bf0dd836-8945-46db-b0dd-0d749d6cd291",
- "version": 9
+ "uuid": "2cecfdac-23c8-45ce-b618-08789216c3bc",
+ "version": 2
}
\ No newline at end of file
diff --git a/workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-Re-organize-STAR-solo-output.ga b/workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-Re-organize-STAR-solo-output.ga
deleted file mode 100644
index 5cf1c91d3..000000000
--- a/workflows/transcriptomics/sc-rnaseq/Galaxy-Workflow-Re-organize-STAR-solo-output.ga
+++ /dev/null
@@ -1,570 +0,0 @@
-{
- "a_galaxy_workflow": "true",
- "annotation": "This workflows re organize the output of STAR solo to have a list:list collection where each identifier is the sample name and inside there are 3 items: matrix.mtx, barcodes.tsv, and features.tsv",
- "creator": [
- {
- "class": "Person",
- "identifier": "https://orcid.org/0000-0002-1964-4960",
- "name": "Lucille Delisle"
- }
- ],
- "format-version": "0.1",
- "license": "MIT",
- "name": "Re-organize-STAR-solo-output",
- "steps": {
- "0": {
- "annotation": "Collection named Genes raw or Genes filtered from STARsolo output",
- "content_id": null,
- "errors": null,
- "id": 0,
- "input_connections": {},
- "inputs": [
- {
- "description": "Collection named Genes raw or Genes filtered from STARsolo output",
- "name": "STARsolo Genes"
- }
- ],
- "label": "STARsolo Genes",
- "name": "Input dataset collection",
- "outputs": [],
- "position": {
- "bottom": 289.8000030517578,
- "height": 61.80000305175781,
- "left": 13,
- "right": 213,
- "top": 228,
- "width": 200,
- "x": 13,
- "y": 228
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
- "tool_version": null,
- "type": "data_collection_input",
- "uuid": "3e312de3-0895-4b46-ac51-9c1c7e341194",
- "workflow_outputs": []
- },
- "1": {
- "annotation": "Collection named Barcodes raw or Barcodes filtered from STARsolo output",
- "content_id": null,
- "errors": null,
- "id": 1,
- "input_connections": {},
- "inputs": [
- {
- "description": "Collection named Barcodes raw or Barcodes filtered from STARsolo output",
- "name": "STARsolo Barcodes"
- }
- ],
- "label": "STARsolo Barcodes",
- "name": "Input dataset collection",
- "outputs": [],
- "position": {
- "bottom": 436.1999969482422,
- "height": 82.19999694824219,
- "left": 36,
- "right": 236,
- "top": 354,
- "width": 200,
- "x": 36,
- "y": 354
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
- "tool_version": null,
- "type": "data_collection_input",
- "uuid": "4f8d1d99-0adc-40a8-a53b-ce9c1c614aeb",
- "workflow_outputs": []
- },
- "2": {
- "annotation": "Collection named Matrix Gene Counts raw or Matrix Gene Counts filtered from STARsolo output",
- "content_id": null,
- "errors": null,
- "id": 2,
- "input_connections": {},
- "inputs": [
- {
- "description": "Collection named Matrix Gene Counts raw or Matrix Gene Counts filtered from STARsolo output",
- "name": "STARsolo Matrix Gene Counts"
- }
- ],
- "label": "STARsolo Matrix Gene Counts",
- "name": "Input dataset collection",
- "outputs": [],
- "position": {
- "bottom": 559.1999969482422,
- "height": 82.19999694824219,
- "left": 97,
- "right": 297,
- "top": 477,
- "width": 200,
- "x": 97,
- "y": 477
- },
- "tool_id": null,
- "tool_state": "{\"optional\": false, \"tag\": null, \"collection_type\": \"list\"}",
- "tool_version": null,
- "type": "data_collection_input",
- "uuid": "266958e3-aacf-4b7f-8f74-6cbcdd5db4c0",
- "workflow_outputs": []
- },
- "3": {
- "annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
- "errors": null,
- "id": 3,
- "input_connections": {
- "input_collection": {
- "id": 2,
- "output_name": "output"
- }
- },
- "inputs": [],
- "label": null,
- "name": "Extract element identifiers",
- "outputs": [
- {
- "name": "output",
- "type": "txt"
- }
- ],
- "position": {
- "bottom": 779.6000061035156,
- "height": 113.60000610351562,
- "left": 350,
- "right": 550,
- "top": 666,
- "width": 200,
- "x": 350,
- "y": 666
- },
- "post_job_actions": {
- "HideDatasetActionoutput": {
- "action_arguments": {},
- "action_type": "HideDatasetAction",
- "output_name": "output"
- }
- },
- "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2",
- "tool_shed_repository": {
- "changeset_revision": "d3c07d270a50",
- "name": "collection_element_identifiers",
- "owner": "iuc",
- "tool_shed": "toolshed.g2.bx.psu.edu"
- },
- "tool_state": "{\"__input_ext\": \"tsv\", \"chromInfo\": \"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\", \"input_collection\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
- "tool_version": "0.0.2",
- "type": "tool",
- "uuid": "ff023a14-a401-4ede-8dfb-2187d2d8ad84",
- "workflow_outputs": []
- },
- "4": {
- "annotation": "",
- "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2",
- "errors": null,
- "id": 4,
- "input_connections": {
- "infile": {
- "id": 3,
- "output_name": "output"
- }
- },
- "inputs": [],
- "label": null,
- "name": "Replace Text",
- "outputs": [
- {
- "name": "outfile",
- "type": "input"
- }
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