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Merge pull request #23 from sven1103/master
Adds profile integration tests
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commit
5395156d22
3 changed files with 30 additions and 0 deletions
28
.travis.yml
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28
.travis.yml
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sudo: required
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language: python
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jdk: openjdk8
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services:
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- docker
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python:
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- '3.6'
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cache: pip
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matrix:
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fast_finish: true
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before_install:
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# PRs to master are only ok if coming from dev branch
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- '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ])'
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install:
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# Install Nextflow
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- mkdir /tmp/nextflow && cd /tmp/nextflow
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- wget -qO- get.nextflow.io | bash
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- sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
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env:
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- NXF_VER='18.10.1' # Specify a minimum NF version that should be tested and work
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- NXF_VER='' # Plus: get the latest NF version and check, that it works
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script:
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# Run the pipeline with the test profile and test remote config
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- nextflow run nf-core/hlatyping --custom_config_version ${TRAVIS_BRANCH} -profile test_configs,test,docker
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1
conf/test_configs.config
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1
conf/test_configs.config
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// Empty config for integration test purposes.
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@ -22,6 +22,7 @@ profiles {
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munin { includeConfig "${params.custom_config_base}/munin.config" }
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phoenix { includeConfig "${params.custom_config_base}/phoenix.config" }
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shh { includeConfig "${params.custom_config_base}/shh.config" }
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test_configs { includeConfig "${params.custom_config_base}/test_configs.config"}
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uct_hex { includeConfig "${params.custom_config_base}/uct_hex.config" }
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uppmax_devel { includeConfig "${params.custom_config_base}/uppmax.config"
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includeConfig "${params.custom_config_base}/uppmax-devel.config"
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