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update bcftools concat #16241

update bcftools concat

update bcftools concat #16241

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` tests to ensure that the module code meets the nf-core guidelines
on:
push:
branches: [master]
pull_request:
branches: [master]
# Cancel if a newer run is started
concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true
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@v3
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
- name: Install nf-core tools
run: python -m pip install nf-core
- 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@v3
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}
restore-keys: |
${{ runner.os }}