From e3a4ec2b1184bf5e2b2a4bfdc4ecd6c52831d07a Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Mon, 17 Feb 2025 15:08:39 +0000 Subject: [PATCH 1/2] update download ci --- .github/workflows/download_pipeline.yml | 28 ++++++++++++------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 77dce0a..544a6b7 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -12,14 +12,6 @@ on: required: true default: "dev" pull_request: - types: - - opened - - edited - - synchronize - branches: - - main - - master - pull_request_target: branches: - main - master @@ -29,7 +21,7 @@ env: jobs: configure: - runs-on: ubuntu-latest + runs-on: ubuntu-latest{% raw %} outputs: REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} @@ -40,7 +32,7 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}" download: runs-on: gpu @@ -73,7 +65,7 @@ jobs: - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./singularity_container_images + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images{% raw %} run: | nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ @@ -85,10 +77,10 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %} - name: Inspect container images - run: tree ./singularity_container_images | tee ./container_initial + run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %} - name: Count the downloaded number of container images id: count_initial @@ -120,6 +112,7 @@ jobs: echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts + id: count_comparison run: | if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} @@ -131,4 +124,11 @@ jobs: exit 1 else echo "The pipeline can be downloaded successfully!" - fi + fi{% endraw %} + + - name: Upload Nextflow logfile for debugging purposes + uses: actions/upload-artifact@v4 + with: + name: nextflow_logfile.txt + path: .nextflow.log* + include-hidden-files: true{% endif %} From 15c0430f11bae54b8bc9c77b83acfae0f7395c28 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Mon, 17 Feb 2025 15:10:53 +0000 Subject: [PATCH 2/2] update download ci --- .github/workflows/download_pipeline.yml | 20 ++++++-------------- 1 file changed, 6 insertions(+), 14 deletions(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 544a6b7..b642725 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -21,7 +21,7 @@ env: jobs: configure: - runs-on: ubuntu-latest{% raw %} + runs-on: ubuntu-latest outputs: REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} @@ -32,7 +32,7 @@ jobs: run: | echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" download: runs-on: gpu @@ -65,7 +65,7 @@ jobs: - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./singularity_container_images{% raw %} + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ @@ -77,10 +77,10 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} - name: Inspect container images - run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %} + run: tree ./singularity_container_images | tee ./container_initial - name: Count the downloaded number of container images id: count_initial @@ -112,7 +112,6 @@ jobs: echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts - id: count_comparison run: | if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} @@ -124,11 +123,4 @@ jobs: exit 1 else echo "The pipeline can be downloaded successfully!" - fi{% endraw %} - - - name: Upload Nextflow logfile for debugging purposes - uses: actions/upload-artifact@v4 - with: - name: nextflow_logfile.txt - path: .nextflow.log* - include-hidden-files: true{% endif %} + fi