Merge pull request #655 from planemo-autoupdate/workflows/scRNAseq/fa…

…stq-to-matrix-10x Updating workflows/scRNAseq/fastq-to-matrix-10x from 0.5 to 0.6
galaxyproject · Feb 6, 2025 · c55fea0 · c55fea0
2 parents 624689b + 610e717
commit c55fea0
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diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md b/workflows/scRNAseq/fastq-to-matrix-10x/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.6] 2025-01-27
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0`
+
 ## [0.5] 2024-09-25
 
 ### Manual update

diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex-tests.yml
@@ -56,7 +56,7 @@
     MultiQC_STARsolo:
       asserts:
         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>"
+          expression: "<td class=\"data-coloured star-uniquely_mapped_percent \"><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):
       attributes: { collection_type: list:list }
       element_tests:

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
@@ -31,7 +31,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.5",
+    "release": "0.6",
     "name": "scRNA-seq_preprocessing_10X_cellPlex",
     "steps": {
         "0": {
@@ -575,7 +575,7 @@
                         },
                         "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
                         "tool_shed_repository": {
-                            "changeset_revision": "45795f582ae9",
+                            "changeset_revision": "381a32c51141",
                             "name": "rna_starsolo",
                             "owner": "iuc",
                             "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -589,7 +589,7 @@
                     },
                     "6": {
                         "annotation": "",
-                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
+                        "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
                         "errors": null,
                         "id": 6,
                         "input_connections": {
@@ -626,15 +626,15 @@
                                 "output_name": "stats"
                             }
                         },
-                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
+                        "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
                         "tool_shed_repository": {
-                            "changeset_revision": "f7e2f1eb3a16",
+                            "changeset_revision": "a7e081ceb76a",
                             "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": "1.24.1+galaxy0",
+                        "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": "1.27+galaxy0",
                         "type": "tool",
                         "uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973",
                         "when": null,
@@ -1297,7 +1297,7 @@
                                 }
                             },
                             "tags": [],
-                            "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a"
+                            "uuid": "06f30f06-b69c-4ea3-90e4-147ecc94e793"
                         },
                         "tool_id": null,
                         "type": "subworkflow",
@@ -1313,7 +1313,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "a999ad68-faa9-4ccb-81b4-ac648af028bd"
+                "uuid": "757efad5-5a3c-4c2b-b4d1-0df04b199eb6"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -2096,7 +2096,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "79342c4e-bb7a-4b25-a214-7d5a10fbfd79"
+                "uuid": "382870e4-d51b-4286-9ca4-ffb2c60d9349"
             },
             "tool_id": null,
             "type": "subworkflow",

diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3-tests.yml
@@ -31,7 +31,7 @@
     'MultiQC on input dataset(s): Webpage':
       asserts:
         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>"
+          expression: "<td class=\"data-coloured star-uniquely_mapped_percent \"><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):
       attributes: { collection_type: list:list }
       element_tests:

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
@@ -30,7 +30,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.5",
+    "release": "0.6",
     "name": "scRNA-seq_preprocessing_10X_v3_Bundle",
     "steps": {
         "0": {
@@ -280,12 +280,12 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo/rna_starsolo/2.7.11a+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "45795f582ae9",
+                "changeset_revision": "381a32c51141",
                 "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\"}, \"sjdbGTFfeatureExon\": \"exon\", \"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\", \"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_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",
@@ -294,7 +294,7 @@
         },
         "6": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
             "errors": null,
             "id": 6,
             "input_connections": {
@@ -331,15 +331,15 @@
                     "output_name": "stats"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.27+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "f7e2f1eb3a16",
+                "changeset_revision": "a7e081ceb76a",
                 "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": "1.24.1+galaxy0",
+            "tool_version": "1.27+galaxy0",
             "type": "tool",
             "uuid": "a16bf20e-2bc9-45e7-a0a3-b5590212b973",
             "when": null,
@@ -1002,7 +1002,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "933626df-33e9-46ac-8206-d297a7fcb83a"
+                "uuid": "a659bfa0-c80f-41f2-b0cd-ce7cf192af61"
             },
             "tool_id": null,
             "type": "subworkflow",