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Add custom java truststore support and improved exception handling #223

Add custom java truststore support and improved exception handling

Add custom java truststore support and improved exception handling #223

Workflow file for this run

name: nf-aggregate linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: actions/setup-node@v3
- 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@v3
- uses: actions/setup-node@v3
- name: Install Prettier
run: npm install -g prettier
- name: Run Prettier --check
run: prettier --check ${GITHUB_WORKSPACE}
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Check code lints with Black
uses: psf/black@stable
# If the above check failed, post a comment on the PR explaining the failure
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v1
with:
message: |
## Python linting (`black`) is failing
To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:
* Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
* Fix formatting errors in your pipeline: `black .`
Once you push these changes the test should pass, and you can hide this comment :+1:
We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
Thanks again for your contribution!
repo-token: ${{ secrets.GITHUB_TOKEN }}
allow-repeats: false
nf-core:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # 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@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
with:
name: linting-logs
path: |
lint_log.txt
lint_results.md
PR_number.txt