diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md index 7d6476cb7..a9f83bd6b 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md +++ b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md @@ -1,5 +1,13 @@ # Changelog +## [0.2] 2024-02-05 + +### Tool updates +- `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy4` +- `pick_value` was replaced by `toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0` + + + ## [0.1] 2023-12-21 First release. diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga index bf8a89fcb..f6c7b6977 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex.ga @@ -30,7 +30,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "scRNA-seq_preprocessing_10X_cellPlex", "steps": { "0": { @@ -50,7 +50,7 @@ "outputs": [], "position": { "left": 0, - "top": 0.0 + "top": 0 }, "tool_id": null, "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}", @@ -289,8 +289,8 @@ "name": "scRNA-seq_preprocessing_10X_v3_Bundle", "outputs": [], "position": { - "left": 651.7833251953125, - "top": 121.58331298828125 + "left": 662.4507693654512, + "top": 75.05904568073197 }, "subworkflow": { "a_galaxy_workflow": "true", @@ -342,7 +342,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 0 }, "tool_id": null, @@ -463,7 +463,7 @@ }, "5": { "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": 5, "input_connections": { @@ -488,12 +488,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool RNA STARSolo", - "name": "sc" - } - ], + "inputs": [], "label": null, "name": "RNA STARSolo", "outputs": [ @@ -567,15 +562,15 @@ "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__\": \"RuntimeValue\"}, \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"RuntimeValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"RuntimeValue\"}, \"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": "2.7.10b+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\": {\"__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": "2.7.10b+galaxy4", "type": "tool", "uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5", "when": null, @@ -1285,7 +1280,7 @@ ] } }, - "tags": "#single-cell", + "tags": ["#single-cell"], "uuid": "600e9a1d-4fd3-4351-8427-4fbd215af136" }, "tool_id": null, @@ -1301,23 +1296,23 @@ ] } }, - "tags": "#single-cell", - "uuid": "f448bde9-4c4a-4a73-a81c-c5cc4f92cb25" + "tags": ["#single-cell"], + "uuid": "19feac09-8db7-4e3f-9774-8b815918cfa7" }, "tool_id": null, "type": "subworkflow", - "uuid": "54892686-893b-4553-bb06-a03714cd4cb4", + "uuid": "20cd1d79-f289-40d5-a239-ef1f18c0df35", "when": null, "workflow_outputs": [ - { - "label": "MultiQC_STARsolo", - "output_name": "MultiQC on input dataset(s): Webpage", - "uuid": "197cee04-2824-4da0-88da-1a73498dcb5b" - }, { "label": "Seurat input for gene expression (filtered)", "output_name": "Seurat input for gene expression (filtered)", - "uuid": "9d063fd4-de07-4840-ad9f-d6956016d71b" + "uuid": "1fc82f04-a2b3-4036-b07f-09e27045d251" + }, + { + "label": "MultiQC_STARsolo", + "output_name": "MultiQC on input dataset(s): Webpage", + "uuid": "84c213a8-9b9a-413e-b944-be94e6ac80ac" } ] }, @@ -1435,7 +1430,7 @@ }, "10": { "annotation": "", - "content_id": "pick_value", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, "id": 10, "input_connections": { @@ -1450,7 +1445,7 @@ "outputs": [ { "name": "data_param", - "type": "data" + "type": "input" } ], "position": { @@ -1466,9 +1461,15 @@ "output_name": "data_param" } }, - "tool_id": "pick_value", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0", + "tool_version": "0.2.0", "type": "tool", "uuid": "c67e69ba-ebd3-4331-9e8e-a9d8c99c3ae6", "when": null, @@ -2081,7 +2082,7 @@ ] } }, - "tags": "#single-cell", + "tags": ["#single-cell"], "uuid": "600e9a1d-4fd3-4351-8427-4fbd215af136" }, "tool_id": null, @@ -2098,7 +2099,7 @@ }, "13": { "annotation": "", - "content_id": "pick_value", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", "errors": null, "id": 13, "input_connections": { @@ -2113,7 +2114,7 @@ "outputs": [ { "name": "data_param", - "type": "data" + "type": "input" } ], "position": { @@ -2129,9 +2130,15 @@ "output_name": "data_param" } }, - "tool_id": "pick_value", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0", + "tool_shed_repository": { + "changeset_revision": "b19e21af9c52", + "name": "pick_value", + "owner": "iuc", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"style_cond\": {\"pick_style\": \"first\", \"__current_case__\": 0, \"type_cond\": {\"param_type\": \"data\", \"__current_case__\": 4, \"pick_from\": [{\"__index__\": 0, \"value\": {\"__class__\": \"ConnectedValue\"}}]}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.1.0", + "tool_version": "0.2.0", "type": "tool", "uuid": "3e819040-a643-4aa7-949c-42becbf21edd", "when": null, @@ -2147,6 +2154,6 @@ "tags": [ "#single-cell" ], - "uuid": "b3e54a19-09b1-4e6f-b44f-9f7ba8fea0e5", + "uuid": "b8bd25f7-caa3-44da-8329-26dce6d46636", "version": 4 } \ No newline at end of file diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga index 5a0c7cc19..f84c1d6e2 100644 --- a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga +++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3.ga @@ -30,7 +30,7 @@ ], "format-version": "0.1", "license": "MIT", - "release": "0.1", + "release": "0.2", "name": "scRNA-seq_preprocessing_10X_v3_Bundle", "steps": { "0": { @@ -49,7 +49,7 @@ "name": "Input dataset collection", "outputs": [], "position": { - "left": 0.0, + "left": 0, "top": 0 }, "tool_id": null, @@ -170,7 +170,7 @@ }, "5": { "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": 5, "input_connections": { @@ -195,12 +195,7 @@ "output_name": "output" } }, - "inputs": [ - { - "description": "runtime parameter for tool RNA STARSolo", - "name": "sc" - } - ], + "inputs": [], "label": null, "name": "RNA STARSolo", "outputs": [ @@ -274,15 +269,15 @@ "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__\": \"RuntimeValue\"}, \"sjdbOverhang\": \"100\"}}, \"sc\": {\"solo_type\": \"CB_UMI_Simple\", \"__current_case__\": 0, \"input_types\": {\"use\": \"list_paired\", \"__current_case__\": 1, \"input_collection\": {\"__class__\": \"RuntimeValue\"}}, \"soloCBwhitelist\": {\"__class__\": \"RuntimeValue\"}, \"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": "2.7.10b+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\": {\"__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": "2.7.10b+galaxy4", "type": "tool", "uuid": "cef740b0-fa95-4542-b08f-dbfca4bfb3e5", "when": null, @@ -992,7 +987,7 @@ ] } }, - "tags": "#single-cell", + "tags": ["#single-cell"], "uuid": "600e9a1d-4fd3-4351-8427-4fbd215af136" }, "tool_id": null, @@ -1011,6 +1006,6 @@ "tags": [ "#single-cell" ], - "uuid": "f448bde9-4c4a-4a73-a81c-c5cc4f92cb25", - "version": 1 + "uuid": "19feac09-8db7-4e3f-9774-8b815918cfa7", + "version": 2 } \ No newline at end of file