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: ...@@ -16,7 +16,6 @@ variables:
- env - env
- ls -laht - ls -laht
- whoami - whoami
- set -x
### All base jobs. ### All base jobs.
...@@ -85,8 +84,8 @@ astrocyte_test: ...@@ -85,8 +84,8 @@ astrocyte_test:
paths: paths:
- $CI_PROJECT_DIR/workflow/.nextflow.log - $CI_PROJECT_DIR/workflow/.nextflow.log
# This runs the workflow, opting to use Docker containers.
# This runs the workflow, opting to use Docker containers.
docker_astrocyte_test: docker_astrocyte_test:
stage: test_docker stage: test_docker
variables: variables:
...@@ -95,11 +94,15 @@ docker_astrocyte_test: ...@@ -95,11 +94,15 @@ docker_astrocyte_test:
script: script:
- sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml - sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
- echo "Run astrocyte using dockerhub/docker.io registry pulls" - echo "Run astrocyte using dockerhub/docker.io registry pulls"
- nextflow -C ./${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 - astrocyte_cli run "$CI_PROJECT_DIR" --option=q
- test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount" - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
tags: tags:
- cluster_node - cluster_node
artifacts:
reports:
dotenv: build.env
cache_docker_image: cache_docker_image:
stage: cache_docker stage: cache_docker
......
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