Update Pipeline Versions file GH Actions

.github/workflows/update_versions_file.yml

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+# This is a github action that will update a file named “pipeline_versions.txt” (or create if it doesn’t exist) with the following content: 
+# tab-delimited with columns  “pipeline name”, “version”, “date of last commit”. 
+
+name: Update Pipeline Versions
+on:
+  push:
+    branches:
+      - master
+      - develop #added develop to make sure this is working before a release
+  # uncomment for testing
+  # pull_request:
+  #   branches:
+  #     - develop
+  workflow_dispatch:
+
+jobs:
+  update_versions:
+    runs-on: ubuntu-latest
+
+    steps:
+      # This step checks out the code - explicitly fetch the history and checkout the branch to enable us to push files back to the repo
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.head_ref }} # This fetches the branch name that triggered the workflow
+          fetch-depth: 0 # This fetches all history for all branches and tags
+
+      # This step sets up Python environment
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+
+      # This step updates a a file called "pipeline_versions.txt" with the names, versions, and last commit dates of all the pipelines found in the 
+      # "warp/pipelines" directory by parsing the contents of the "*.changelog.md" files.
+      - name: Update Pipeline Versions
+        run: |
+          echo "Current directory: "
+          pwd
+          ls -lht
+          echo -e "Pipeline Name\tVersion\tDate of Last Commit" > pipeline_versions.txt
+          find pipelines -name "*.changelog.md" -type f | while read -r file; do
+            pipeline_name=$(basename "$file" .changelog.md)
+            version=$(head -n 1 "$file" | sed 's/#//')
+            last_commit_date=$(sed -n '2p' "$file" | sed 's/([^)]*)//g')
+            echo -e "$pipeline_name\t$version\t$last_commit_date" >> pipeline_versions.txt
+          done
+
+      # This step commits and pushes the changes to the repository
+      - name: Commit and push changes
+        run: |
+          git config --local user.email "[email protected]"
+          git config --local user.name "GitHub Action"
+          git add pipeline_versions.txt
+          git commit -m "Update pipeline versions"
+          git push
+

pipeline_versions.txt

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+Pipeline Name	Version	Date of Last Commit
+MultiSampleSmartSeq2	 2.2.21	2023-04-19 
+SmartSeq2SingleSample	 5.1.20	2023-04-19 
+snm3C	 4.0.0	2024-03-15 
+Optimus	 7.1.0	2024-05-20 
+scATAC	 1.3.2	2023-08-03 
+MultiSampleSmartSeq2SingleNucleus	 1.3.4	2024-04-12 
+SlideSeq	 3.1.6	2024-05-20 
+BuildIndices	 3.0.0	2023-12-06 
+PairedTag	 0.7.0	2024-05-20
+atac	 2.0.0	2024-05-20 
+Multiome	 5.0.0	2024-05-20 
+CEMBA	 1.1.6	2023-12-18 
+BuildCembaReferences	 1.0.0	2020-11-15 
+IlluminaGenotypingArray	 1.12.17	2024-03-26 
+ExomeReprocessing	 3.1.19	2024-03-26 
+WholeGenomeReprocessing	 3.1.20	2024-03-26 
+ExternalExomeReprocessing	 3.1.21	2024-03-26 
+ExternalWholeGenomeReprocessing	 2.1.21	2024-03-26 
+CramToUnmappedBams	 1.1.2	2022-04-14 
+AnnotationFiltration	 1.2.5	2023-12-18 
+BroadInternalUltimaGenomics	 1.0.17	2024-03-26 
+BroadInternalRNAWithUMIs	 1.0.29	2024-03-26 
+BroadInternalImputation	 1.1.10	2023-12-18 
+BroadInternalArrays	 1.1.7	2024-03-26 
+UltimaGenomicsWholeGenomeCramOnly	 1.0.16	2024-03-26 
+GDCWholeGenomeSomaticSingleSample	 1.3.1	2024-01-19 
+VariantCalling	 2.1.18	2024-03-26 
+JointGenotyping	 1.6.10	2023-12-18 
+JointGenotypingByChromosomePartOne	 1.4.12	2023-12-18 
+JointGenotypingByChromosomePartTwo	 1.4.11	2023-12-18 
+UltimaGenomicsJointGenotyping	 1.1.7	2023-12-18 
+ReblockGVCF	 2.1.12	2024-03-26 
+ExomeGermlineSingleSample	 3.1.19	2024-03-26 
+UltimaGenomicsWholeGenomeGermline	 1.0.16	2024-03-26 
+WholeGenomeGermlineSingleSample	 3.1.20	2024-03-26 
+RNAWithUMIsPipeline	 1.0.16	2023-12-18 
+CheckFingerprint	 1.0.16	2024-03-26 
+ValidateChip	 1.16.4	2023-12-18 
+Imputation	 1.1.12	2023-12-18 
+MultiSampleArrays	 1.6.1	2022-04-14 
+Arrays	 2.6.23	2024-03-26