sudo: required language: python jdk: openjdk8 services: - docker python: - '3.6' cache: pip matrix: fast_finish: true 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 - mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests env: - NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config. - NXF_VER='' SCRATCH='~' # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config. script: # Run the pipeline with the test profile and test remote config - | grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \ tr -s ' ' | \ cut -d " " -f 2 | \ grep -v "czbiohub_aws" | \ xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf --custom_config_base=${TRAVIS_BUILD_DIR} -profile {}