Merge branch 'dev' of https://github.com/nf-core/rnaseq into strand

Author: drpatelh

.github/workflows/fix-linting.yml

@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "name=result::pass" >> $GITHUB_OUTPUT
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "name=result::fail" >> $GITHUB_OUTPUT
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "name=pr_number::$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

workflows/rnaseq.nf

@@ -786,7 +786,7 @@ workflow RNASEQ {
     // MODULE: Pipeline reporting
     //
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_versions.unique{ it.text }.collectFile(name: 'collated_versions.yml')
+        ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 
     //