From 6f10eacd0c64e5311d14e3c90d6ae70971ca6647 Mon Sep 17 00:00:00 2001
From: planemo-autoupdate <planemo-autoupdate@users.noreply.github.com>
Date: Mon, 23 Dec 2024 05:55:46 +0000
Subject: [PATCH] Updating workflows/transcriptomics/rnaseq-sr from 1.1 to 1.2

---
 .../transcriptomics/rnaseq-sr/CHANGELOG.md    |  5 +++++
 .../transcriptomics/rnaseq-sr/rnaseq-sr.ga    | 20 +++++++++----------
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md b/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md
index 20acc310a..014689882 100644
--- a/workflows/transcriptomics/rnaseq-sr/CHANGELOG.md
+++ b/workflows/transcriptomics/rnaseq-sr/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] 2024-11-25
 
 ### Automatic update
diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga
index ffc320d6c..4efd72089 100644
--- a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga
+++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr.ga
@@ -79,7 +79,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "1.1",
+    "release": "1.2",
     "name": "RNA-seq for Single-read 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"
@@ -781,7 +781,7 @@
             },
             "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"
@@ -1144,7 +1144,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "71d32e61-70bd-4571-b3a4-79cc4d726233"
+                "uuid": "19346ffc-c7c7-4542-852f-64416ee3d249"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1731,7 +1731,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "5626e8b4-2709-4f0f-9dd9-bc05f8b35222"
+                "uuid": "c61d63de-d2f2-466d-b036-f3cea13e5cdf"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -1747,7 +1747,7 @@
         },
         "19": {
             "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": 19,
             "input_connections": {
@@ -1802,15 +1802,15 @@
                     "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\": \"single_end\", \"__current_case__\": 0}, \"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)",
@@ -2512,7 +2512,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "aead7b4c-1b24-43d4-a44d-fc51b143e669"
+                "uuid": "972ae8f9-8275-47dc-8b0f-47966f174f05"
             },
             "tool_id": null,
             "type": "subworkflow",
@@ -3331,7 +3331,7 @@
                     }
                 },
                 "tags": [],
-                "uuid": "4a006f05-4ee3-4bbe-ab82-7d9489c378c0"
+                "uuid": "1ef923d0-43ee-47e4-b597-df3777db86ff"
             },
             "tool_id": null,
             "type": "subworkflow",