.travis.yml

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 onuryukselen/rnaseq:3.0
  # Fake the tag locally so that the pipeline runs properly
  - docker tag onuryukselen/rnaseq:3.0 dolphinnext/rnaseq:3.0
  

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
  # Download sample files
  - mkdir inputs && cd inputs && wget https://galaxyweb.umassmed.edu/pub/dnext_data/test/reads/control_rep1.1.fastq.gz https://galaxyweb.umassmed.edu/pub/dnext_data/test/reads/exper_rep1.1.fastq.gz  && cd ..
  # Install markdownlint-cli
  - sudo apt-get install npm && npm install -g markdownlint-cli
  


env:
  - NXF_VER='19.04.1' # 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:
  # Start Test Run
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker