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prettier and added test_AA_local profile to test AA and AS locally wi… #464

prettier and added test_AA_local profile to test AA and AS locally wi…

prettier and added test_AA_local profile to test AA and AS locally wi… #464

Workflow file for this run

name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` and markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.11
uses: actions/setup-python@v5
with:
python-version: 3.11
cache: "pip"
- name: Install pre-commit
run: pip install pre-commit
- name: Run pre-commit
run: pre-commit run --all-files
nf-core:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
- uses: actions/setup-python@v5
with:
python-version: "3.11"
architecture: "x64"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install nf-core
- name: Run nf-core lint
env:
GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
- name: Save PR number
if: ${{ always() }}
run: echo ${{ github.event.pull_request.number }} > PR_number.txt
- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@v4
with:
name: linting-logs
path: |
lint_log.txt
lint_results.md
PR_number.txt