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GeT-nextflow-NGL-Bi
wf-Illumina-nf
Commits
0e47a70b
Commit
0e47a70b
authored
Feb 12, 2021
by
Celine Noirot
Browse files
add test workflow in CI
parent
4974b176
Pipeline
#37598
failed
Changes
1
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1
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.gitlab-ci.yml
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0e47a70b
# recipe for building singularity image and deploy it on the registery for bwa version 0.7.17
image
:
name
:
quay.io/singularity/singularity:v3.4.0
entrypoint
:
[
"
"
]
stages
:
-
build
-
deploy
-
test
# Build Singularity container bwa_v0.7.17.sif
singularity-image
:
# recipe for building singularity image and deploy it on the registery for bwa version 0.7.17
image
:
name
:
quay.io/singularity/singularity:v3.4.0
stage
:
build
script
:
-
singularity build template.sif Singularityfile
...
...
@@ -23,6 +22,8 @@ singularity-image:
# Push the image template.sif on the registry
deploy
:
image
:
name
:
quay.io/singularity/singularity:v3.4.0
stage
:
deploy
script
:
-
singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" template.sif oras://"$CI_REGISTRY_IMAGE"/"$CI_PROJECT_NAME":"$CI_COMMIT_TAG"
...
...
@@ -30,4 +31,13 @@ deploy:
changes
:
-
.gitlab-ci.yml
-
Singularityfile
-
emvironement.yml
\ No newline at end of file
-
emvironement.yml
test
:
image
:
nextflow/nextflow
stage
:
test
push
:
script
:
-
git clone git clone git@forgemia.inra.fr:get-nextflow-ngl-bi/template-nf.git
-
cd template-nf
-
ln -s template.sif template-nf.sif
-
nextflow run main.nf -profile test,singularity
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