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Adds in GitHub Actions tests

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Alexander Peltzer 2019-11-26 00:25:49 +01:00
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4 changed files with 52 additions and 34 deletions

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.github/linting.yml vendored Normal file
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@ -0,0 +1,20 @@
name: Markdown linting
# This workflow is triggered on pushes and PRs to the repository.
on: [push, pull_request]
jobs:
Markdown:
runs-on: ubuntu-18.04
steps:
- uses: actions/checkout@v1
- uses: actions/setup-node@v1
with:
node-version: '10'
- name: Install markdownlint
run: |
npm install -g markdownlint-cli
- name: Run Markdownlint
run: |
markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml

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.github/main.yml vendored Normal file
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name: nfcore configs tests
## Check whether users added their config to the matrix
on: [push, pull_request]
paths:
- '.github/main.workflow'
jobs:
job_1:
name: Run individual profiles
strategy:
matrix:
profile: ['awsbatch, bigpurple, binac, cbe, ccga_dx, ccga, cfc, crick, czbiohub_aws_highpriority, czbiohub_aws, denbi_qbic, genouest, gis, hebbe, kraken, munin, pasteur, phoenix, prince, shh, uct_hex, uppmax_devel, uppmax, uzh']
steps:
- uses: actions/checkout@v1
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Check ${{ matrix.profile }} profile
run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}

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sudo: required
language: python
jdk: openjdk8
services:
- docker
python:
- '3.6'
cache: pip
matrix:
fast_finish: true
install:
# Install Nextflow
- mkdir /tmp/nextflow && cd /tmp/nextflow
- wget -qO- get.nextflow.io | bash
- sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
- mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
env:
- NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
- NXF_VER='' SCRATCH='~' # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config.
script:
# Run the pipeline with the test profile and test remote config
- |
grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
tr -s ' ' | \
cut -d " " -f 2 | \
grep -v "czbiohub_aws" | \
xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf --custom_config_base=${TRAVIS_BUILD_DIR} -profile {}

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# ![nf-core/configs](docs/images/nfcore-configs_logo.png)
[![Build Status](https://travis-ci.org/nf-core/configs.svg?branch=master)](https://travis-ci.org/nf-core/configs)
[![Lint Status](https://github.com/nf-core/config/workflows/nfcore%20configs%20tests/badge.svg)](https://github.com/nf-core/config/workflows/nfcore%20configs%20tests/badge.svg)
A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
## Table of contents
* [Using an existing config](#using-an-existing-config)
* [!nf-core/configs](#nf-coreconfigs)
* [Table of contents](#table-of-contents)
* [Using an existing config](#using-an-existing-config)
* [Configuration and parameters](#configuration-and-parameters)
* [Offline usage](#offline-usage)
* [Adding a new config](#adding-a-new-config)
* [Adding a new config](#adding-a-new-config)
* [Checking user hostnames](#checking-user-hostnames)
* [Testing](#testing)
* [Documentation](#documentation)
* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
* [Help](#help)
* [Help](#help)
## Using an existing config
@ -111,6 +115,8 @@ Currently documentation is available for the following systems:
[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/configs` repository to your own GitHub account. Within the local clone of your fork add the custom config file to the [`conf/`](https://github.com/nf-core/configs/tree/master/conf) directory, and the documentation file to the [`docs/`](https://github.com/nf-core/configs/tree/master/docs) directory. You will also need to edit and add your custom profile to the [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) file in the top-level directory of the clone.
Afterwards, make sure to edit the `.github/main.yml` file and add your profile name to alphabetically sorted `profile:` scope. This way, it will be tested automatically using GitHub Actions.
Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on the `nf-core/configs` GitHub repo with the appropriate information.
We will be notified automatically when you have created your pull request, and providing that everything adheres to nf-core guidelines we will endeavour to approve your pull request as soon as possible.