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Adds in GitHub Actions tests
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4 changed files with 52 additions and 34 deletions
20
.github/linting.yml
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.github/linting.yml
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name: Markdown linting
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# This workflow is triggered on pushes and PRs to the repository.
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on: [push, pull_request]
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jobs:
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Markdown:
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runs-on: ubuntu-18.04
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steps:
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- uses: actions/checkout@v1
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- uses: actions/setup-node@v1
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with:
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node-version: '10'
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- name: Install markdownlint
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run: |
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npm install -g markdownlint-cli
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- name: Run Markdownlint
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run: |
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markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml
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22
.github/main.yml
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.github/main.yml
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name: nfcore configs tests
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## Check whether users added their config to the matrix
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on: [push, pull_request]
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paths:
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- '.github/main.workflow'
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jobs:
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job_1:
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name: Run individual profiles
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strategy:
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matrix:
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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']
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steps:
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- uses: actions/checkout@v1
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- name: Install Nextflow
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Check ${{ matrix.profile }} profile
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run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}
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30
.travis.yml
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.travis.yml
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sudo: required
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language: python
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jdk: openjdk8
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services:
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- docker
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python:
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- '3.6'
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cache: pip
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matrix:
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fast_finish: true
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install:
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# Install Nextflow
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- mkdir /tmp/nextflow && cd /tmp/nextflow
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- wget -qO- get.nextflow.io | bash
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- sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
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- mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
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env:
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- NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
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- NXF_VER='' SCRATCH='~' # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config.
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script:
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# Run the pipeline with the test profile and test remote config
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- |
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grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
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tr -s ' ' | \
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cut -d " " -f 2 | \
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grep -v "czbiohub_aws" | \
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xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf --custom_config_base=${TRAVIS_BUILD_DIR} -profile {}
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14
README.md
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README.md
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# ![nf-core/configs](docs/images/nfcore-configs_logo.png)
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[![Build Status](https://travis-ci.org/nf-core/configs.svg?branch=master)](https://travis-ci.org/nf-core/configs)
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[![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)
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A repository for hosting nextflow config files containing custom parameters required to run nf-core pipelines at different Institutions.
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## Table of contents
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* [Using an existing config](#using-an-existing-config)
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* [!nf-core/configs](#nf-coreconfigs)
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* [Table of contents](#table-of-contents)
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* [Using an existing config](#using-an-existing-config)
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* [Configuration and parameters](#configuration-and-parameters)
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* [Offline usage](#offline-usage)
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* [Adding a new config](#adding-a-new-config)
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* [Adding a new config](#adding-a-new-config)
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* [Checking user hostnames](#checking-user-hostnames)
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* [Testing](#testing)
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* [Documentation](#documentation)
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* [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs)
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* [Help](#help)
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* [Help](#help)
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## Using an existing config
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@ -111,6 +115,8 @@ Currently documentation is available for the following systems:
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[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.
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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.
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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.
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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.
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