Commit 98e548ff authored by Devin OKelly's avatar Devin OKelly
Browse files

Test step-dependent nextflow configs.

parent 27dfa945
......@@ -47,13 +47,23 @@ astrocyte_check:
script:
- astrocyte_cli check "$CI_PROJECT_DIR"
nextflow_test:
nextflow_test_docker:
stage: test
script:
- module load nextflow/20.01.0
- module load singularity/3.5.3
- cd $CI_PROJECT_DIR/workflow
- nextflow -C $CI_PROJECT_DIR/workflow/configs/biohpc.config run main.nf -with-trace -with-timeline -resume --verbose
- nextflow -C $CI_PROJECT_DIR/workflow/configs/biohpc_docker.config run main.nf -with-trace -with-timeline -resume --verbose
nextflow_test_singularity:
stage: test
script:
- module load nextflow/20.01.0
- module load singularity/3.5.3
- cd $CI_PROJECT_DIR/workflow
- nextflow -C $CI_PROJECT_DIR/workflow/configs/biohpc_singularity.config run main.nf -with-trace -with-timeline -resume --verbose
# This runs the workflow with test data and does a simple
# check for the expected output file
......@@ -68,6 +78,7 @@ astrocyte_test:
docker_astrocyte_test:
stage: test_docker
script:
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
- echo "Run astrocyte using dockerhub/docker.io registry pulls"
cache_docker_image:
......
docker {
enabled = true
}
process {
executor = 'local'
}
singularity {
enabled = true
runOptions = '--bind /vagrant:/vagrant'
cacheDir = "$baseDir/images/singularity"
}
process {
executor = 'local'
}
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