From 49d36810dd4aa5eb69126bc239eacd4a8ec1cea9 Mon Sep 17 00:00:00 2001
From: Nicolas Descostes <nicolas.descostes@embl.it>
Date: Thu, 14 Apr 2022 16:50:11 +0200
Subject: [PATCH] replace by main

---
 .gitlab-ci.yml                                | 49 +++----------------
 .../fastqc/Singularity.fastqc-0119cv8         |  1 -
 .../image-analysis/deeplabcut-deploy.yaml     |  9 ++++
 .../image-analysis/deeplabcut-test.backup     |  6 +++
 yaml-files/quality-control/fastqc-test.backup | 21 ++++++++
 5 files changed, 44 insertions(+), 42 deletions(-)
 create mode 100644 yaml-files/image-analysis/deeplabcut-deploy.yaml
 create mode 100644 yaml-files/image-analysis/deeplabcut-test.backup
 create mode 100644 yaml-files/quality-control/fastqc-test.backup

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index edd3958..88585d2 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 d32654e..d891b73 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 0000000..94cff85
--- /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 0000000..451aa06
--- /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 0000000..e7ad88c
--- /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/
-- 
GitLab