Commit b1bdbe74 authored by Devin OKelly's avatar Devin OKelly
Browse files

Update .gitlab-ci.yml file

[ci skip]
parent 6c7d6267
......@@ -16,7 +16,6 @@ variables:
- env
- ls -laht
- whoami
- set -x
### All base jobs.
......@@ -85,8 +84,8 @@ astrocyte_test:
paths:
- $CI_PROJECT_DIR/workflow/.nextflow.log
# This runs the workflow, opting to use Docker containers.
# This runs the workflow, opting to use Docker containers.
docker_astrocyte_test:
stage: test_docker
variables:
......@@ -95,11 +94,15 @@ docker_astrocyte_test:
script:
- sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
- echo "Run astrocyte using dockerhub/docker.io registry pulls"
- nextflow -C ./${config_path}/${config_filename} config -flat
- nextflow -C ./configs/biohpc_docker.config config -flat | grep -oP "process\.'[\w:]+'\.container = '\K([\w:]+)(?=')" | uniq >> containers.txt
- echo "BUILD_VERSION=hello" >> build.env
- astrocyte_cli run "$CI_PROJECT_DIR" --option=q
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
tags:
- cluster_node
artifacts:
reports:
dotenv: build.env
cache_docker_image:
stage: cache_docker
......
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