.travis.yml

sudo: required
language: java
jdk: openjdk8
services:
  - docker
python:
  - "2.7"
cache: pip
matrix:
  fast_finish: true

before_install:
  # Pull the docker image first so the test doesn't wait for this
  - docker pull nfcore/methylseq
  # Fake the tag locally so that the pipeline runs properly
  - docker tag nfcore/methylseq nfcore/methylseq:1.1

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
  - git clone https://github.com/nf-core/tools.git /tmp/nf-core-tools
  - cd /tmp/nf-core-tools
  - pip install --user -e .
  # Reset
  - mkdir ${TRAVIS_BUILD_DIR}/tests
  - cd ${TRAVIS_BUILD_DIR}/tests

env:
  - ALIGNER=bismark NXF_VER=0.30.0
  - ALIGNER=bismark
  - ALIGNER=bwameth NXF_VER=0.30.0
  - ALIGNER=bwameth

script:
  # Lint the pipeline code
  - nf-core lint ${TRAVIS_BUILD_DIR}
  # Run, build reference genome
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --aligner $ALIGNER --saveReference
  # Basic run with supplied reference
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --aligner $ALIGNER ${TRAVIS_BUILD_DIR}/tests/results/reference_genome/BismarkIndex/
  # Run, RRBS mode with no trimming
  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --aligner $ALIGNER --notrim --rrbs