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https://github.com/MillironX/nf-configs.git
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fb60856e40
Previously travis tests could only succeed if the config was already present in the master branch, but for newly added configs it would always fail. This commit sets custom_config_base to the local clone of the PR branch on the Travis VM where the file is present.
30 lines
999 B
YAML
30 lines
999 B
YAML
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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- mkdir -p ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
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env:
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- NXF_VER='18.10.1' SCRATCH='~' # Specify a minimum NF version that should be tested and work. Set SCRATCH for prince.config.
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- NXF_VER='' SCRATCH='~' # Plus: get the latest NF version and check, that it works. Set SCRATCH for prince.config.
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script:
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# Run the pipeline with the test profile and test remote config
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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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grep -v "czbiohub_aws" | \
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xargs -I {} nextflow run ${TRAVIS_BUILD_DIR}/configtest.nf --custom_config_base=${TRAVIS_BUILD_DIR} -profile {}
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