From a525ce9f1f34d4951e04a4fe066272c1780b482d Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 24 Feb 2025 13:56:32 +0100 Subject: [PATCH 1/2] fix udpate_components script --- .github/workflows/update_components_template.yml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml index 575065d383..04a2143025 100644 --- a/.github/workflows/update_components_template.yml +++ b/.github/workflows/update_components_template.yml @@ -12,14 +12,23 @@ jobs: steps: - name: Checkout repository uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 + with: + ref: dev - name: Set up Python uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.x" + - name: Install Nextflow + uses: nf-core/setup-nextflow@v2 + with: + version: "24.04.2" + - name: Install nf-core - run: pip install nf-core + run: | + python -m pip install --upgrade pip + pip install . - name: Update modules run: nf-core modules update --all --no-preview @@ -36,11 +45,11 @@ jobs: git config user.name "nf-core-bot" git add . git status - git commit -m "[automated] Fix code linting" + git commit -m "[automated] Update components in template" # Open a new PR to dev with the changes - name: Create PR run: | git checkout -b update-modules git push origin update-modules - gh pr create --title "Update modules in template" --body "This PR updates the modules in the pipeline template" --base dev --head update-modules + gh pr create --title "Template: Update components in template" --body "This PR updates the modules and subworkflows in the pipeline template" --base dev --head update-modules From 6f63caa80d428983c84a4e31aa5b0eac3b7b1816 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 24 Feb 2025 15:20:42 +0100 Subject: [PATCH 2/2] remove component update script --- .../workflows/update_components_template.yml | 55 ------------------- 1 file changed, 55 deletions(-) delete mode 100644 .github/workflows/update_components_template.yml diff --git a/.github/workflows/update_components_template.yml b/.github/workflows/update_components_template.yml deleted file mode 100644 index 04a2143025..0000000000 --- a/.github/workflows/update_components_template.yml +++ /dev/null @@ -1,55 +0,0 @@ -name: Update Modules Template - -on: - schedule: - - cron: "0 0 * * *" - workflow_dispatch: - -jobs: - update_modules: - runs-on: ubuntu-latest - - steps: - - name: Checkout repository - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - with: - ref: dev - - - name: Set up Python - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 - with: - python-version: "3.x" - - - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 - with: - version: "24.04.2" - - - name: Install nf-core - run: | - python -m pip install --upgrade pip - pip install . - - - name: Update modules - run: nf-core modules update --all --no-preview - working-directory: nf_core/pipeline-template - - - name: Update subworkflows - run: nf-core subworkflows update --all --no-preview - working-directory: nf_core/pipeline-template - - # Commit the changes - - name: Commit changes - run: | - git config user.email "core@nf-co.re" - git config user.name "nf-core-bot" - git add . - git status - git commit -m "[automated] Update components in template" - - # Open a new PR to dev with the changes - - name: Create PR - run: | - git checkout -b update-modules - git push origin update-modules - gh pr create --title "Template: Update components in template" --body "This PR updates the modules and subworkflows in the pipeline template" --base dev --head update-modules