Commit 4d5ee3b9 authored by Devin OKelly's avatar Devin OKelly
Browse files

Merge CI changes and add more parsing to the CI pipeline

parent 34827e55
......@@ -85,11 +85,16 @@ astrocyte_test:
- $CI_PROJECT_DIR/workflow/.nextflow.log
# This runs the workflow, opting to use Docker containers.
docker_astrocyte_test:
stage: test_docker
variables:
config_path : "workflow/configs/"
config_filename : "biohpc_docker.config"
script:
- sed -i 's|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27biohpc_docker.config\x27|' astrocyte_pkg.yml
- sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
- echo "Run astrocyte using dockerhub/docker.io registry pulls"
- nextflow -C ./${config_path}/${config_filename} config -flat
- astrocyte_cli run "$CI_PROJECT_DIR" --option=q
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
tags:
......
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