2019-03-06 16:42:14 +00:00
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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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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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2019-03-06 19:11:20 +00:00
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- mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
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2019-03-06 16:42:14 +00:00
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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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2019-03-12 16:25:16 +00:00
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- |
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grep "{.*includeConfig.*[a-z]*\.config\"" ${TRAVIS_BUILD_DIR}/nfcore_custom.config | \
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tr -s ' ' | \
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cut -d " " -f 2 | \
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xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf -profile {}
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