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fixes start of code block #50

fixes start of code block

fixes start of code block #50

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:
pull_request:
release:
types: [published]
jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v2
- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
- name: Run ECLint check
run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/setup-node@v2
- name: Install Prettier
run: npm install -g prettier
- name: Run Prettier --check
run: prettier --check ${GITHUB_WORKSPACE}
nf-core:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Install Nextflow
env:
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- uses: actions/setup-python@v3
with:
python-version: "3.6"
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@v2
with:
name: linting-logs
path: |
lint_log.txt
lint_results.md
PR_number.txt