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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,67 @@ | ||
name: Test successful pipeline download with 'nf-core download' | ||
|
||
# Run the workflow when: | ||
# - dispatched manually | ||
# - 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: | ||
workflow_dispatch: | ||
pull_request: | ||
types: | ||
- opened | ||
branches: | ||
- master | ||
pull_request_target: | ||
branches: | ||
- master | ||
|
||
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: "3.11" | ||
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 |
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@@ -4,7 +4,7 @@ on: | |
types: [created] | ||
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||
jobs: | ||
deploy: | ||
fix-linting: | ||
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
if: > | ||
contains(github.event.comment.html_url, '/pull/') && | ||
|
@@ -13,43 +13,77 @@ jobs: | |
runs-on: ubuntu-latest | ||
steps: | ||
# Use the @nf-core-bot token to check out so we can push later | ||
- uses: actions/checkout@v4 | ||
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | ||
with: | ||
token: ${{ secrets.nf_core_bot_auth_token }} | ||
|
||
# indication that the linting is being fixed | ||
- name: React on comment | ||
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
with: | ||
comment-id: ${{ github.event.comment.id }} | ||
reactions: eyes | ||
|
||
# Action runs on the issue comment, so we don't get the PR by default | ||
# Use the gh cli to check out the PR | ||
- name: Checkout Pull Request | ||
run: gh pr checkout ${{ github.event.issue.number }} | ||
env: | ||
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
|
||
- uses: actions/setup-node@v4 | ||
# Install and run pre-commit | ||
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | ||
with: | ||
python-version: 3.11 | ||
|
||
- name: Install Prettier | ||
run: npm install -g prettier @prettier/plugin-php | ||
- name: Install pre-commit | ||
run: pip install pre-commit | ||
|
||
# Check that we actually need to fix something | ||
- name: Run 'prettier --check' | ||
id: prettier_status | ||
run: | | ||
if prettier --check ${GITHUB_WORKSPACE}; then | ||
echo "result=pass" >> $GITHUB_OUTPUT | ||
else | ||
echo "result=fail" >> $GITHUB_OUTPUT | ||
fi | ||
- name: Run pre-commit | ||
id: pre-commit | ||
run: pre-commit run --all-files | ||
continue-on-error: true | ||
|
||
- name: Run 'prettier --write' | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
run: prettier --write ${GITHUB_WORKSPACE} | ||
# indication that the linting has finished | ||
- name: react if linting finished succesfully | ||
if: steps.pre-commit.outcome == 'success' | ||
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
with: | ||
comment-id: ${{ github.event.comment.id }} | ||
reactions: "+1" | ||
|
||
- name: Commit & push changes | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
id: commit-and-push | ||
if: steps.pre-commit.outcome == 'failure' | ||
run: | | ||
git config user.email "[email protected]" | ||
git config user.name "nf-core-bot" | ||
git config push.default upstream | ||
git add . | ||
git status | ||
git commit -m "[automated] Fix linting with Prettier" | ||
git commit -m "[automated] Fix code linting" | ||
git push | ||
- name: react if linting errors were fixed | ||
id: react-if-fixed | ||
if: steps.commit-and-push.outcome == 'success' | ||
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
with: | ||
comment-id: ${{ github.event.comment.id }} | ||
reactions: hooray | ||
|
||
- name: react if linting errors were not fixed | ||
if: steps.commit-and-push.outcome == 'failure' | ||
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
with: | ||
comment-id: ${{ github.event.comment.id }} | ||
reactions: confused | ||
|
||
- name: react if linting errors were not fixed | ||
if: steps.commit-and-push.outcome == 'failure' | ||
uses: peter-evans/create-or-update-comment@71345be0265236311c031f5c7866368bd1eff043 # v4 | ||
with: | ||
issue-number: ${{ github.event.issue.number }} | ||
body: | | ||
@${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. | ||
See [CI log](https://github.com/nf-core/scrnaseq/actions/runs/${{ github.run_id }}) for more details. |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,5 +1,10 @@ | ||
repos: | ||
- repo: https://github.com/pre-commit/mirrors-prettier | ||
rev: "v2.7.1" | ||
rev: "v3.1.0" | ||
hooks: | ||
- id: prettier | ||
- repo: https://github.com/editorconfig-checker/editorconfig-checker.python | ||
rev: "2.7.3" | ||
hooks: | ||
- id: editorconfig-checker | ||
alias: ec |
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