mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
f34892c1af
* Update functions.nf for publish_by_id * Pass a list of publish_by_id instead of a string * Remove NF version * Rename code linting file * Run separate workflow for nf-core modules lint * Adjust nf-core update comment * Comment out linting from pytest-workflow.yml * Remove commented out linting code from pytest-workflow.yml * Adjust spacing * Adjust spacing again * Move NF version to job level for linting * Add CAPSULE_LOG none env when installing NF * Remove NXF_ANSI_LOG env for linting * Revert changes
75 lines
2.1 KiB
YAML
75 lines
2.1 KiB
YAML
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, pull_request]
|
|
|
|
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@v2
|
|
|
|
- uses: dorny/paths-filter@v2
|
|
id: filter
|
|
with:
|
|
filters: 'tests/config/pytest_software.yml'
|
|
|
|
lint:
|
|
runs-on: ubuntu-20.04
|
|
env:
|
|
NXF_VER: 21.03.0-edge
|
|
|
|
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@v2
|
|
|
|
- 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
|
|
|
|
# FIXME: Remove this when nf-core modules lint stabilizes and install stable release
|
|
- name: Install nf-core tools development version
|
|
run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
|
|
|
|
- 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 . -t ${{ matrix.tags }}
|
|
|
|
- uses: actions/cache@v2
|
|
with:
|
|
path: /usr/local/bin/nextflow
|
|
key: ${{ runner.os }}
|
|
restore-keys: |
|
|
${{ runner.os }}
|