✨ add new module: seqkit/rmdup #59
Workflow file for this run
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name: nf-core linting | |
# This workflow is triggered on pushes and PRs to the repository. | |
# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines | |
on: | |
push: | |
branches: [master] | |
pull_request: | |
branches: [master] | |
jobs: | |
changes: | |
name: Check for changes | |
runs-on: ubuntu-latest | |
outputs: | |
# Expose matched filters as job 'modules' output variable | |
modules: ${{ steps.filter.outputs.changes }} | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: dorny/paths-filter@v2 | |
id: filter | |
with: | |
filters: "tests/config/pytest_modules.yml" | |
lint: | |
runs-on: ubuntu-20.04 | |
name: ${{ matrix.tags }} | |
needs: changes | |
if: needs.changes.outputs.modules != '[]' | |
strategy: | |
fail-fast: false | |
matrix: | |
tags: ["${{ fromJson(needs.changes.outputs.modules) }}"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: "3.x" | |
- uses: actions/cache@v2 | |
with: | |
path: ~/.cache/pip | |
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} | |
restore-keys: | | |
${{ runner.os }}-pip- | |
- name: Set up Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: "3.x" | |
- name: Install pip | |
run: python -m pip install --upgrade pip | |
# Install a nf-core/tools custom release | |
- name: Install nf-core tools development version | |
run: python -m pip install --upgrade --force-reinstall git+https://github.com/bunop/tools.git@custom-modules | |
- name: Install Nextflow | |
env: | |
CAPSULE_LOG: none | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Lint ${{ matrix.tags }} | |
run: nf-core modules lint ${{ matrix.tags }} | |
# HACK | |
if: startsWith( matrix.tags, 'subworkflow' ) != true | |
- uses: actions/cache@v2 | |
with: | |
path: /usr/local/bin/nextflow | |
key: ${{ runner.os }} | |
restore-keys: | | |
${{ runner.os }} |