diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index edd39585acc054bd5b1aca6e23647914e90964c8..88585d20280ec493b45091fc06a48e3161fae807 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -30,55 +30,22 @@ image: - singularity build container.sif $RECIPE_PATH/Singularity.$BASENAME-$TAG - singularity push --docker-username gitlab-ci-token --docker-password $CI_JOB_TOKEN container.sif oras://"$CI_REGISTRY_IMAGE"/$BASENAME:$TAG - ##################### -# Image analysis +## Submission area ##################### -#deeplabcut-2202-test: -# extends: .templateTest -# variables: -# BASENAME: deeplabcut -# TAG: 2202 -# RECIPE_PATH: recipes/image-analysis/deeplabcut +## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST -deeplabcut-2202-builddeploy: - extends: .templateBuildDeploy - variables: - BASENAME: deeplabcut - TAG: 2202 - RECIPE_PATH: recipes/image-analysis/deeplabcut - only: - changes: - - recipes/image-analysis/deeplabcut/Singularity.deeplabcut-2202 +##################### +# Image analysis +##################### +include: + - local: "yaml-files/image-analysis/deeplabcut-deploy.yaml" ##################### ## Quality control ##################### -#fastqc-0119cv7-test: -# extends: .templateTest -# variables: -# BASENAME: fastqc -# TAG: 0119cv7 -# RECIPE_PATH: recipes/quality-control/fastqc/ - - -#fastqc-0119cv8-test: -# extends: .templateTest -# variables: -# BASENAME: fastqc -# TAG: 0119cv8 -# RECIPE_PATH: recipes/quality-control/fastqc/ - -#fastqc-0119cv6-test: -# extends: .templateTest -# variables: -# BASENAME: fastqc -# TAG: 0119cv6 -# RECIPE_PATH: recipes/quality-control/fastqc/ - - include: - - local: yaml-files/quality-control/fastqc-deploy.yaml + - local: "yaml-files/quality-control/fastqc-deploy.yaml" diff --git a/recipes/quality-control/fastqc/Singularity.fastqc-0119cv8 b/recipes/quality-control/fastqc/Singularity.fastqc-0119cv8 index d32654ed2f220f5f3263cf797e226b878e007aa2..d891b73c36b562bd228f1f74a3b513b5f3a619a8 100644 --- a/recipes/quality-control/fastqc/Singularity.fastqc-0119cv8 +++ b/recipes/quality-control/fastqc/Singularity.fastqc-0119cv8 @@ -10,4 +10,3 @@ From: biocontainers/fastqc:v0.11.9_cv8 %labels Author Nicolas Descostes - diff --git a/yaml-files/image-analysis/deeplabcut-deploy.yaml b/yaml-files/image-analysis/deeplabcut-deploy.yaml new file mode 100644 index 0000000000000000000000000000000000000000..94cff85ce4055151a41d7d4180268a73512a754a --- /dev/null +++ b/yaml-files/image-analysis/deeplabcut-deploy.yaml @@ -0,0 +1,9 @@ +deeplabcut-2202-builddeploy: + extends: .templateBuildDeploy + variables: + BASENAME: deeplabcut + TAG: 2202 + RECIPE_PATH: recipes/image-analysis/deeplabcut + only: + changes: + - recipes/image-analysis/deeplabcut/Singularity.deeplabcut-2202 diff --git a/yaml-files/image-analysis/deeplabcut-test.backup b/yaml-files/image-analysis/deeplabcut-test.backup new file mode 100644 index 0000000000000000000000000000000000000000..451aa069ea5cf2f6e02fd4e8f37f3a366f7500d8 --- /dev/null +++ b/yaml-files/image-analysis/deeplabcut-test.backup @@ -0,0 +1,6 @@ +deeplabcut-2202-test: + extends: .templateTest + variables: + BASENAME: deeplabcut + TAG: 2202 + RECIPE_PATH: recipes/image-analysis/deeplabcut diff --git a/yaml-files/quality-control/fastqc-test.backup b/yaml-files/quality-control/fastqc-test.backup new file mode 100644 index 0000000000000000000000000000000000000000..e7ad88ca552cd5344e2b4c3f21063e4c680fbb9c --- /dev/null +++ b/yaml-files/quality-control/fastqc-test.backup @@ -0,0 +1,21 @@ +fastqc-0119cv7-test: + extends: .templateTest + variables: + BASENAME: fastqc + TAG: 0119cv7 + RECIPE_PATH: recipes/quality-control/fastqc/ + + +fastqc-0119cv8-test: + extends: .templateTest + variables: + BASENAME: fastqc + TAG: 0119cv8 + RECIPE_PATH: recipes/quality-control/fastqc/ + +fastqc-0119cv6-test: + extends: .templateTest + variables: + BASENAME: fastqc + TAG: 0119cv6 + RECIPE_PATH: recipes/quality-control/fastqc/