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Updated modules and subworkflows #24

Updated modules and subworkflows

Updated modules and subworkflows #24

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