.travis.yml

sudo: required
language: java
jdk: openjdk8
services: docker

addons:
  apt:
    update: true

env:
  global:
    - NXF_VER=0.32.0
  matrix:
    - TEST=SOMATIC
    - TEST=GERMLINE
    - TEST=ANNOTATEVEP
    - TEST=ANNOTATESNPEFF

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" ])'
# Donwload containers
  - "travis_retry ./scripts/containers.sh --profile docker --test $TEST"

install:
  # Install Nextflow
  - curl -fsSL get.nextflow.io | bash
  - chmod +x nextflow
  - sudo mv nextflow /usr/local/bin/

# Build references if needed
before_script: "./scripts/test.sh --profile docker --test $TEST --build"

# Actual tests
script: "./scripts/test.sh --profile docker --test $TEST"