Merge branch 'develop' into release/0.2.4

Author: buehlere

.github/CODEOWNERS

@@ -3,18 +3,22 @@
 modules/msk/calculatenoise/** @mikefeixu @mskcc-omics-workflows/reviewers
 modules/msk/custom/splitfastqbylane/** @anoronh4 @mskcc-omics-workflows/reviewers
 modules/msk/facets/** @nikhil @mskcc-omics-workflows/reviewers
+modules/msk/fgbio/collectduplexseqmetrics/** @mikefeixu @mskcc-omics-workflows/reviewers
 modules/msk/gatk4/applybqsr/** @yocra3 @FriederikeHanssen @mskcc-omics-workflows/reviewers
 modules/msk/gbcms/** @buehlere @mskcc-omics-workflows/reviewers
+modules/msk/generatemutfasta/1.1/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
+modules/msk/generatemutfasta/1.2/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/genomenexus/annotationpipeline/** @rnaidu @mskcc-omics-workflows/reviewers
 modules/msk/genomenexus/vcf2maf/** @rnaidu @mskcc-omics-workflows/reviewers
 modules/msk/genotypevariants/all/** @buehlere @mskcc-omics-workflows/reviewers
+modules/msk/mutalyzer/normalizer/** @nikhil @mskcc-omics-workflows/reviewers
+modules/msk/mutalyzer/retriever/** @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/mutect1/** @rnaidu @mskcc-omics-workflows/reviewers
 modules/msk/neoantigenediting/aligntoiedb/** @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/neoantigenediting/computefitness/** @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/neoantigenutils/convertannotjson/** @johnoooh @mskcc-omics-workflows/reviewers
 modules/msk/neoantigenutils/formatnetmhcpan/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/neoantigenutils/generatehlastring/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
-modules/msk/neoantigenutils/generatemutfasta/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/neoantigenutils/neoantigeninput/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/neosv/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/netmhc3/** @johnoooh @nikhil @mskcc-omics-workflows/reviewers
@@ -33,6 +37,7 @@ modules/msk/rediscoverte/** @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/salmon/index/** @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/salmon/quant/** @nikhil @mskcc-omics-workflows/reviewers
 modules/msk/snppileup/** @nikhil @mskcc-omics-workflows/reviewers
+subworkflows/msk/generate_mutated_peptides/**  @mskcc-omics-workflows/reviewers
 subworkflows/msk/genome_nexus/** @rnaidu @mskcc-omics-workflows/reviewers
 subworkflows/msk/neoantigen_editing/** @johnoooh @mskcc-omics-workflows/reviewers
 subworkflows/msk/netmhcstabandpan/** @nikhil @mskcc-omics-workflows/reviewers

.github/workflows/assign_codeowners.yml

@@ -11,24 +11,45 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
         with:
-          repository: ${{ github.event.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.ref }}
-      - name: Install yq
+          token: ${{ secrets.ACTION_TOKEN }}
+          persist-credentials: false
+
+      - name: Install yq and fd-find
         run: |
           sudo snap install yq
-          sudo apt install fd-find
+          sudo apt update
+          sudo apt install -y fd-find
+          # Create alias for fd-find
+          echo "alias fd=fdfind" >> ~/.bashrc
+          source ~/.bashrc
+
       - name: Run generate_codeowners.sh
         run: |
           chmod +x .github/generate_codeowners.sh
           ./.github/generate_codeowners.sh
+
       - name: Validate codeowners file
         uses: mszostok/codeowners-validator@v0.7.4
         with:
           checks: "files,duppatterns,syntax"
-      - name: Commit CODEOWNERS changes
-        uses: EndBug/add-and-commit@v9
-        with:
-          add: '[".github/CODEOWNERS --force"]'
-          message: "Update CODEOWNERS file"
-          default_author: github_actions
-          cwd: "./"
+
+      - name: Check for CODEOWNERS changes
+        id: check_changes
+        run: |
+          if git diff --exit-code .github/CODEOWNERS; then
+            echo "changed=false" >> $GITHUB_OUTPUT
+          else
+            echo "changed=true" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Commit and push changes
+        if: steps.check_changes.outputs.changed == 'true'
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+          git add .github/CODEOWNERS
+          git commit -m "update CODEOWNERS file"
+
+          git remote set-url origin "https://x-access-token:${{ secrets.ACTION_TOKEN }}@github.com/mskcc-omics-workflows/modules.git"
+          git push --force-with-lease origin develop