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sudo: required
language: python
jdk: openjdk8
services: docker
python: '3.6'
cache: pip
matrix:
fast_finish: true
before_install:
# PRs to master are only ok if coming from dev branch
- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
# Pull the docker image first so the test doesn't wait for this
- docker pull nfcore/hic:dev
# Fake the tag locally so that the pipeline runs properly
# Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
- docker tag nfcore/hic:dev nfcore/hic:dev
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
# Install nf-core/tools
- pip install --upgrade pip
- pip install nf-core
# Reset
- mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
# Install markdownlint-cli
- sudo apt-get install npm && npm install -g markdownlint-cli
env:
- NXF_VER='0.32.0' # Specify a minimum NF version that should be tested and work
- NXF_VER='' # Plus: get the latest NF version and check that it works
script:
# Lint the pipeline code
- nf-core lint ${TRAVIS_BUILD_DIR}
# Lint the documentation
- markdownlint ${TRAVIS_BUILD_DIR} -c ${TRAVIS_BUILD_DIR}/.github/markdownlint.yml
# Run the pipeline with the test profile
- nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker