Updating workflows/transcriptomics/rnaseq-pe from 1.1 to 1.2

galaxyproject · Dec 23, 2024 · 70d64be · 70d64be
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diff --git a/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md b/workflows/transcriptomics/rnaseq-pe/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changelog
 
+## [1.2] 2024-12-23
+
+### Automatic update
+- `toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.8+galaxy0`
+
 ## [1.1] 2024-11-18
 
 ### Automatic update

diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe.ga
@@ -79,7 +79,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "1.1",
+    "release": "1.2",
     "name": "RNA-seq for Paired-end fastqs",
     "report": {
         "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n"
@@ -851,7 +851,7 @@
             },
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy1",
             "tool_shed_repository": {
-                "changeset_revision": "4014de1b6daf",
+                "changeset_revision": "53255f6eecfc",
                 "name": "rgrnastar",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -1214,7 +1214,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "7abe9e86-1aea-4cc5-bbc3-8a98e09f0bc6"
+                "uuid": "eeb556ab-fa7d-4ca5-ae19-c77deee9d11d"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1801,7 +1801,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "d2af388a-2469-44c1-ad24-ef9511546b8e"
+                "uuid": "25393782-f44b-4f80-be08-a27a7927dc71"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1817,7 +1817,7 @@
         },
         "21": {
             "annotation": "",
-            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0",
+            "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.8+galaxy0",
             "errors": null,
             "id": 21,
             "input_connections": {
@@ -1872,15 +1872,15 @@
                     "output_name": "output_summary"
                 }
             },
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.6+galaxy0",
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.8+galaxy0",
             "tool_shed_repository": {
-                "changeset_revision": "1b851f87fbe0",
+                "changeset_revision": "5dbff3a5845a",
                 "name": "featurecounts",
                 "owner": "iuc",
                 "tool_shed": "toolshed.g2.bx.psu.edu"
             },
             "tool_state": "{\"alignment\": {\"__class__\": \"ConnectedValue\"}, \"anno\": {\"anno_select\": \"history\", \"__current_case__\": 2, \"reference_gene_sets\": {\"__class__\": \"ConnectedValue\"}, \"gff_feature_type\": \"exon\", \"gff_feature_attribute\": \"gene_id\", \"summarization_level\": false}, \"extended_parameters\": {\"multifeatures\": {\"multifeat\": \"\", \"__current_case__\": 0}, \"exon_exon_junction_read_counting_enabled\": {\"count_exon_exon_junction_reads\": \"\", \"__current_case__\": 1}, \"long_reads\": false, \"by_read_group\": false, \"largest_overlap\": false, \"min_overlap\": \"1\", \"frac_overlap\": \"0\", \"frac_overlap_feature\": \"0\", \"read_extension_5p\": \"0\", \"read_extension_3p\": \"0\", \"read_reduction\": \"\", \"R\": false}, \"format\": \"tabdel_short\", \"include_feature_length_file\": false, \"pe_parameters\": {\"paired_end_status\": \"PE_fragments\", \"__current_case__\": 2, \"check_distance_enabled\": {\"checkFragLength\": \"false\", \"__current_case__\": 1}, \"only_both_ends\": false, \"exclude_chimerics\": true}, \"read_filtering_parameters\": {\"mapping_quality\": \"0\", \"splitonly\": \"\", \"primary\": false, \"ignore_dup\": false}, \"strand_specificity\": {\"__class__\": \"ConnectedValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
-            "tool_version": "2.0.6+galaxy0",
+            "tool_version": "2.0.8+galaxy0",
             "type": "tool",
             "uuid": "5a03b546-eb3f-4e99-b845-24c8f54ed183",
             "when": "$(inputs.when)",
@@ -2566,7 +2566,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "de2ecd60-7f89-4062-8db5-60406bc79148"
+                "uuid": "992d6156-5a55-4a73-a92e-0de4c158c7ef"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -3385,7 +3385,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "4e0fb735-1e3f-4948-8991-001ef7d7e7c0"
+                "uuid": "697a6065-b1fa-4f6a-a86a-5c7876abb26b"
             },
             "tool_id": null,
             "type": "subworkflow",