Commit 0e47a70b authored by Celine Noirot's avatar Celine Noirot
Browse files

add test workflow in CI

parent 4974b176
Pipeline #26376 failed
# 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: stages:
- build - build
- deploy - deploy
- test
# Build Singularity container bwa_v0.7.17.sif # Build Singularity container bwa_v0.7.17.sif
singularity-image: 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 stage: build
script: script:
- singularity build template.sif Singularityfile - singularity build template.sif Singularityfile
...@@ -23,6 +22,8 @@ singularity-image: ...@@ -23,6 +22,8 @@ singularity-image:
# Push the image template.sif on the registry # Push the image template.sif on the registry
deploy: deploy:
image:
name: quay.io/singularity/singularity:v3.4.0
stage: deploy stage: deploy
script: script:
- singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" template.sif oras://"$CI_REGISTRY_IMAGE"/"$CI_PROJECT_NAME":"$CI_COMMIT_TAG" - singularity push --docker-username "${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: ...@@ -30,4 +31,13 @@ deploy:
changes: changes:
- .gitlab-ci.yml - .gitlab-ci.yml
- Singularityfile - Singularityfile
- emvironement.yml - emvironement.yml
\ No newline at end of file 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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