From 6ea4d62ed918919d187bfbbf0988e12679a0cff3 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Wed, 20 Dec 2023 16:47:55 +0100 Subject: [PATCH 1/4] Add a Github Action Workflow to the pipeline template that tests a successful download. --- CHANGELOG.md | 2 + .../.github/workflows/download_pipeline.yml | 70 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 nf_core/pipeline-template/.github/workflows/download_pipeline.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 8a252cbf67..c6fd827245 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Add a Github Action Workflow to the pipeline template that tests a successful download with 'nf-core download' ([#2618](https://github.com/nf-core/tools/pull/2618)) + ### Download ### Linting diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml new file mode 100644 index 0000000000..7653ac8af4 --- /dev/null +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -0,0 +1,70 @@ +name: Test successful pipeline download with 'nf-core download' + +# Run the workflow when: +# - dispatched manually +# - when a PR is opened or reopened to dev or master branches +# - the head branch of the pull request is updated. (Do we need this?) + +on: + workflow_dispatch: + pull_request: + types: + - opened + branches: + - master + - dev + #pull_request_target: + # branches: + # - master + # - dev + +env: + NXF_ANSI_LOG: false + +jobs: + download: + runs-on: ubuntu-latest + steps: + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + + - uses: actions/setup-python@v5 + with: + python-version: "3.10" + architecture: "x64" + - uses: eWaterCycle/setup-singularity@v7 + with: + singularity-version: 3.8.3 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install git+https://github.com/nf-core/tools.git@dev + + - name: Get the repository name and current branch set as environment variable + run: | + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} + echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV} + + - name: Download the pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + run: | + nf-core download ${{ env.REPO_LOWERCASE }} \ + --revision ${{ env.REPO_BRANCH }} \ + --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + --compress "none" \ + --container-system 'singularity' \ + --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-cache-utilisation 'amend' \ + --download-configuration + + - name: Inspect download + run: tree ./${{ env.REPOTITLE_LOWERCASE }} + + - name: Run the downloaded pipeline + env: + NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results From d4f3dc2c7941f5389c1f365d8f3b60aece10e93e Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Thu, 4 Jan 2024 14:40:20 +0100 Subject: [PATCH 2/4] Only run on self-hosted runners due to space constraints in GitHub hosted runners (large container downloads). --- .../pipeline-template/.github/workflows/download_pipeline.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 7653ac8af4..1577304e7b 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -12,18 +12,16 @@ on: - opened branches: - master - - dev #pull_request_target: # branches: # - master - # - dev env: NXF_ANSI_LOG: false jobs: download: - runs-on: ubuntu-latest + runs-on: ["self-hosted"] steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v1 From f93b9244adfdbf85105c54360c2e9967e51df063 Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Thu, 4 Jan 2024 14:46:56 +0100 Subject: [PATCH 3/4] Since we now limit it to PRs to master, updating a PR branch should be a trigger as well. This only applies to last-minute fixes prior to a pipeline release. --- .../.github/workflows/download_pipeline.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 1577304e7b..820c02bec4 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -3,7 +3,7 @@ name: Test successful pipeline download with 'nf-core download' # Run the workflow when: # - dispatched manually # - when a PR is opened or reopened to dev or master branches -# - the head branch of the pull request is updated. (Do we need this?) +# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: @@ -12,9 +12,9 @@ on: - opened branches: - master - #pull_request_target: - # branches: - # - master + pull_request_target: + branches: + - master env: NXF_ANSI_LOG: false From 9fb5498b7fcc442b2803b8d9462cf9a713990602 Mon Sep 17 00:00:00 2001 From: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> Date: Mon, 8 Jan 2024 15:10:52 +0100 Subject: [PATCH 4/4] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Thanks @mirpedrol ! Co-authored-by: Júlia Mir Pedrol --- .../pipeline-template/.github/workflows/download_pipeline.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index 820c02bec4..d5d0307262 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to dev or master branches +# - when a PR is opened or reopened to master branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: @@ -28,7 +28,7 @@ jobs: - uses: actions/setup-python@v5 with: - python-version: "3.10" + python-version: "3.11" architecture: "x64" - uses: eWaterCycle/setup-singularity@v7 with: