From fe151ea77577c075236c7185df71493084e3cb09 Mon Sep 17 00:00:00 2001 From: Kevin Palis Date: Fri, 28 Jun 2024 11:25:09 -0400 Subject: [PATCH 1/9] Adding the actions file --- .github/workflows/update_versions_file.yml | 53 ++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 .github/workflows/update_versions_file.yml diff --git a/.github/workflows/update_versions_file.yml b/.github/workflows/update_versions_file.yml new file mode 100644 index 0000000000..5d8432e9c7 --- /dev/null +++ b/.github/workflows/update_versions_file.yml @@ -0,0 +1,53 @@ +# 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: + - main + pull_request: + branches: + - develop + workflow_dispatch: + +jobs: + update_versions: + runs-on: ubuntu-latest + + steps: + # This step checks out the code + - name: Checkout repository + uses: actions/checkout@v2 + + # This step sets up Python environment + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: 3.x + + # This step installs the project dependencies + - name: Install dependencies + run: pip install -r requirements.txt + + # 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 "pipeline name\tversion\tdate of last commit" > pipeline_versions.txt + find warp/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 "$pipeline_name\t$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 "action@github.com" + git config --local user.name "GitHub Action" + git add pipeline_versions.txt + git commit -m "Update pipeline versions" + git push + \ No newline at end of file From d8a1422723cc118b5909d438b997fdbd8b30e567 Mon Sep 17 00:00:00 2001 From: Kevin Palis Date: Fri, 28 Jun 2024 11:28:39 -0400 Subject: [PATCH 2/9] Removing unnecessary requirements.txt step --- .github/workflows/update_versions_file.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/update_versions_file.yml b/.github/workflows/update_versions_file.yml index 5d8432e9c7..352c8bb260 100644 --- a/.github/workflows/update_versions_file.yml +++ b/.github/workflows/update_versions_file.yml @@ -25,10 +25,6 @@ jobs: uses: actions/setup-python@v2 with: python-version: 3.x - - # This step installs the project dependencies - - name: Install dependencies - run: pip install -r requirements.txt # 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. From 270434e4d4155c8ace7a906821ecf1ba069192ec Mon Sep 17 00:00:00 2001 From: Kevin Palis Date: Fri, 28 Jun 2024 11:34:15 -0400 Subject: [PATCH 3/9] ensuring that the workflow is operating on an actual branch rather than a detached HEAD --- .github/workflows/update_versions_file.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/update_versions_file.yml b/.github/workflows/update_versions_file.yml index 352c8bb260..64381e84cf 100644 --- a/.github/workflows/update_versions_file.yml +++ b/.github/workflows/update_versions_file.yml @@ -16,9 +16,12 @@ jobs: runs-on: ubuntu-latest steps: - # This step checks out the code + # 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@v2 + uses: actions/checkout@v3 + with: + ref: ${{ github.head_ref }} # This fetches the branch name that triggered the workflow + fetch-depth: 0 # This fetches all history for all branches and tags # This step sets up Python environment - name: Set up Python From 4dcd0035ac9f753fb610e2a1d24bf7a467228886 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 28 Jun 2024 15:34:39 +0000 Subject: [PATCH 4/9] Update pipeline versions --- pipeline_versions.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 pipeline_versions.txt diff --git a/pipeline_versions.txt b/pipeline_versions.txt new file mode 100644 index 0000000000..96b30bede6 --- /dev/null +++ b/pipeline_versions.txt @@ -0,0 +1 @@ +pipeline name\tversion\tdate of last commit From d358b0f8c26f7cd73149b8a5358ae96a40205ba6 Mon Sep 17 00:00:00 2001 From: Kevin Palis Date: Fri, 28 Jun 2024 11:43:00 -0400 Subject: [PATCH 5/9] Figuring out the working directory --- .github/workflows/update_versions_file.yml | 6 ++++-- pipeline_versions.txt | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/update_versions_file.yml b/.github/workflows/update_versions_file.yml index 64381e84cf..008ca89018 100644 --- a/.github/workflows/update_versions_file.yml +++ b/.github/workflows/update_versions_file.yml @@ -33,8 +33,10 @@ jobs: # "warp/pipelines" directory by parsing the contents of the "*.changelog.md" files. - name: Update Pipeline Versions run: | - echo "pipeline name\tversion\tdate of last commit" > pipeline_versions.txt - find warp/pipelines -name "*.changelog.md" -type f | while read -r file; do + echo "Current directory: " + pwd + + find pipelines -name "*.changelog.md" -type f | while read -r file; do pipeline_name=$(basename "$file" .changelog.md) version=$(head -n 1 "$file" | sed 's/#//') last_commit_date=$(sed -n '2p' "$file" | sed 's/([^)]*)//g') diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 96b30bede6..f508ef305f 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -1 +1 @@ -pipeline name\tversion\tdate of last commit +pipeline name version date of last commit From e21788754a626ee097ec7fdeb209b394f6e630da Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 28 Jun 2024 15:43:21 +0000 Subject: [PATCH 6/9] Update pipeline versions --- pipeline_versions.txt | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index f508ef305f..2224ef9989 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -1 +1,42 @@ pipeline name version date of last commit +MultiSampleSmartSeq2\t 2.2.21\t2023-04-19 +SmartSeq2SingleSample\t 5.1.20\t2023-04-19 +snm3C\t 4.0.0\t2024-03-15 +Optimus\t 7.1.0\t2024-05-20 +scATAC\t 1.3.2\t2023-08-03 +MultiSampleSmartSeq2SingleNucleus\t 1.3.4\t2024-04-12 +SlideSeq\t 3.1.6\t2024-05-20 +BuildIndices\t 3.0.0\t2023-12-06 +PairedTag\t 0.7.0\t2024-05-20 +atac\t 2.0.0\t2024-05-20 +Multiome\t 5.0.0\t2024-05-20 +CEMBA\t 1.1.6\t2023-12-18 +BuildCembaReferences\t 1.0.0\t2020-11-15 +IlluminaGenotypingArray\t 1.12.17\t2024-03-26 +ExomeReprocessing\t 3.1.19\t2024-03-26 +WholeGenomeReprocessing\t 3.1.20\t2024-03-26 +ExternalExomeReprocessing\t 3.1.21\t2024-03-26 +ExternalWholeGenomeReprocessing\t 2.1.21\t2024-03-26 +CramToUnmappedBams\t 1.1.2\t2022-04-14 +AnnotationFiltration\t 1.2.5\t2023-12-18 +BroadInternalUltimaGenomics\t 1.0.17\t2024-03-26 +BroadInternalRNAWithUMIs\t 1.0.29\t2024-03-26 +BroadInternalImputation\t 1.1.10\t2023-12-18 +BroadInternalArrays\t 1.1.7\t2024-03-26 +UltimaGenomicsWholeGenomeCramOnly\t 1.0.16\t2024-03-26 +GDCWholeGenomeSomaticSingleSample\t 1.3.1\t2024-01-19 +VariantCalling\t 2.1.18\t2024-03-26 +JointGenotyping\t 1.6.10\t2023-12-18 +JointGenotypingByChromosomePartOne\t 1.4.12\t2023-12-18 +JointGenotypingByChromosomePartTwo\t 1.4.11\t2023-12-18 +UltimaGenomicsJointGenotyping\t 1.1.7\t2023-12-18 +ReblockGVCF\t 2.1.12\t2024-03-26 +ExomeGermlineSingleSample\t 3.1.19\t2024-03-26 +UltimaGenomicsWholeGenomeGermline\t 1.0.16\t2024-03-26 +WholeGenomeGermlineSingleSample\t 3.1.20\t2024-03-26 +RNAWithUMIsPipeline\t 1.0.16\t2023-12-18 +CheckFingerprint\t 1.0.16\t2024-03-26 +ValidateChip\t 1.16.4\t2023-12-18 +Imputation\t 1.1.12\t2023-12-18 +MultiSampleArrays\t 1.6.1\t2022-04-14 +Arrays\t 2.6.23\t2024-03-26 From feb586bfc2fb424bfd096eb649f4bba741ea3da5 Mon Sep 17 00:00:00 2001 From: Kevin Palis Date: Fri, 28 Jun 2024 11:47:22 -0400 Subject: [PATCH 7/9] adding -e to the echo command, you enable the interpretation of backslash escapes --- .github/workflows/update_versions_file.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/update_versions_file.yml b/.github/workflows/update_versions_file.yml index 008ca89018..de3ddb1c5b 100644 --- a/.github/workflows/update_versions_file.yml +++ b/.github/workflows/update_versions_file.yml @@ -35,12 +35,13 @@ jobs: 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' "$file" | sed 's/([^)]*)//g') - echo "$pipeline_name\t$version\t$last_commit_date" >> pipeline_versions.txt + echo -e "$pipeline_name\t$version\t$last_commit_date" >> pipeline_versions.txt done # This step commits and pushes the changes to the repository From dc857f4b7f8ed2e14fc08b0d773c74202716bbb5 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 28 Jun 2024 15:48:41 +0000 Subject: [PATCH 8/9] Update pipeline versions --- pipeline_versions.txt | 84 +++++++++++++++++++++---------------------- 1 file changed, 42 insertions(+), 42 deletions(-) diff --git a/pipeline_versions.txt b/pipeline_versions.txt index 2224ef9989..f21150b6f2 100644 --- a/pipeline_versions.txt +++ b/pipeline_versions.txt @@ -1,42 +1,42 @@ -pipeline name version date of last commit -MultiSampleSmartSeq2\t 2.2.21\t2023-04-19 -SmartSeq2SingleSample\t 5.1.20\t2023-04-19 -snm3C\t 4.0.0\t2024-03-15 -Optimus\t 7.1.0\t2024-05-20 -scATAC\t 1.3.2\t2023-08-03 -MultiSampleSmartSeq2SingleNucleus\t 1.3.4\t2024-04-12 -SlideSeq\t 3.1.6\t2024-05-20 -BuildIndices\t 3.0.0\t2023-12-06 -PairedTag\t 0.7.0\t2024-05-20 -atac\t 2.0.0\t2024-05-20 -Multiome\t 5.0.0\t2024-05-20 -CEMBA\t 1.1.6\t2023-12-18 -BuildCembaReferences\t 1.0.0\t2020-11-15 -IlluminaGenotypingArray\t 1.12.17\t2024-03-26 -ExomeReprocessing\t 3.1.19\t2024-03-26 -WholeGenomeReprocessing\t 3.1.20\t2024-03-26 -ExternalExomeReprocessing\t 3.1.21\t2024-03-26 -ExternalWholeGenomeReprocessing\t 2.1.21\t2024-03-26 -CramToUnmappedBams\t 1.1.2\t2022-04-14 -AnnotationFiltration\t 1.2.5\t2023-12-18 -BroadInternalUltimaGenomics\t 1.0.17\t2024-03-26 -BroadInternalRNAWithUMIs\t 1.0.29\t2024-03-26 -BroadInternalImputation\t 1.1.10\t2023-12-18 -BroadInternalArrays\t 1.1.7\t2024-03-26 -UltimaGenomicsWholeGenomeCramOnly\t 1.0.16\t2024-03-26 -GDCWholeGenomeSomaticSingleSample\t 1.3.1\t2024-01-19 -VariantCalling\t 2.1.18\t2024-03-26 -JointGenotyping\t 1.6.10\t2023-12-18 -JointGenotypingByChromosomePartOne\t 1.4.12\t2023-12-18 -JointGenotypingByChromosomePartTwo\t 1.4.11\t2023-12-18 -UltimaGenomicsJointGenotyping\t 1.1.7\t2023-12-18 -ReblockGVCF\t 2.1.12\t2024-03-26 -ExomeGermlineSingleSample\t 3.1.19\t2024-03-26 -UltimaGenomicsWholeGenomeGermline\t 1.0.16\t2024-03-26 -WholeGenomeGermlineSingleSample\t 3.1.20\t2024-03-26 -RNAWithUMIsPipeline\t 1.0.16\t2023-12-18 -CheckFingerprint\t 1.0.16\t2024-03-26 -ValidateChip\t 1.16.4\t2023-12-18 -Imputation\t 1.1.12\t2023-12-18 -MultiSampleArrays\t 1.6.1\t2022-04-14 -Arrays\t 2.6.23\t2024-03-26 +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 From ef3f6e2ccfd45454870e239f4f0a9fed52e84c51 Mon Sep 17 00:00:00 2001 From: Kevin Palis Date: Fri, 28 Jun 2024 11:53:40 -0400 Subject: [PATCH 9/9] Putting in the final triggers --- .github/workflows/update_versions_file.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/update_versions_file.yml b/.github/workflows/update_versions_file.yml index de3ddb1c5b..19b792bfc9 100644 --- a/.github/workflows/update_versions_file.yml +++ b/.github/workflows/update_versions_file.yml @@ -5,10 +5,12 @@ name: Update Pipeline Versions on: push: branches: - - main - pull_request: - branches: - - develop + - master + - develop #added develop to make sure this is working before a release + # uncomment for testing + # pull_request: + # branches: + # - develop workflow_dispatch: jobs: