Commit 67bc14f5 authored by Devin OKelly's avatar Devin OKelly
Browse files

Update .gitlab-ci.yml file

parent d0e7a849
......@@ -87,9 +87,13 @@ astrocyte_test:
# 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:
......@@ -98,8 +102,9 @@ docker_astrocyte_test:
cache_docker_image:
stage: cache_docker
script:
- docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
- echo $CI_REGISTRY_PASSWORD | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
- echo "Pull Docker image from the docker.io registry, re-tag, and push to our GitLab"
- docker
- echo "Need to know what the docker image is ahead of time"
singularity_astrocyte_test:
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment