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BioHPC
astrocyte_example_wordcount
Commits
0cb47c84
Commit
0cb47c84
authored
Jun 14, 2021
by
Devin OKelly
Browse files
Update .gitlab-ci.yml file
parent
89b79a90
Changes
1
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.gitlab-ci.yml
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0cb47c84
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@@ -94,7 +94,7 @@ docker_astrocyte_test:
script
:
-
sed -i "s|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27${config_filename}\x27|" astrocyte_pkg.yml
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echo "Run astrocyte using dockerhub/docker.io registry pulls"
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nextflow -C
.
/configs/biohpc_docker.config config -flat | grep -oP "process\.'[\w:]+'\.container = '\K([\w:]+)(?=')" | uniq >> containers.txt
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nextflow -C
workflow
/configs/biohpc_docker.config config -flat | grep -oP "process\.'[\w:]+'\.container = '\K([\w:]+)(?=')" | uniq >> containers.txt
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echo "BUILD_VERSION=hello" >> build.env
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astrocyte_cli run "$CI_PROJECT_DIR" --option=q
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test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
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