2019-03-06 16:42:14 +00:00
|
|
|
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" ])'
|
|
|
|
|
|
|
|
|
|
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
|
2019-03-06 19:11:20 +00:00
|
|
|
- mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
|
2019-03-06 16:42:14 +00:00
|
|
|
|
|
|
|
|
env:
|
|
|
|
|
- NXF_VER='18.10.1' # 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:
|
|
|
|
|
# Run the pipeline with the test profile and test remote config
|
2019-03-08 10:58:37 +00:00
|
|
|
- grep "[a-z]*.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | | tr -s ' ' | cut -d " " -f 2 | xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}
|
