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Merge pull request #23 from sven1103/master

Adds profile integration tests
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Sven F 2019-03-06 18:24:48 +01:00 committed by GitHub
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.travis.yml Normal file
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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
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
- nextflow run nf-core/hlatyping --custom_config_version ${TRAVIS_BRANCH} -profile test_configs,test,docker

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conf/test_configs.config Normal file
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// Empty config for integration test purposes.

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@ -22,6 +22,7 @@ profiles {
munin { includeConfig "${params.custom_config_base}/munin.config" }
phoenix { includeConfig "${params.custom_config_base}/phoenix.config" }
shh { includeConfig "${params.custom_config_base}/shh.config" }
test_configs { includeConfig "${params.custom_config_base}/test_configs.config"}
uct_hex { includeConfig "${params.custom_config_base}/uct_hex.config" }
uppmax_devel { includeConfig "${params.custom_config_base}/uppmax.config"
includeConfig "${params.custom_config_base}/uppmax-devel.config"