From bfd85869c0e24c4c36b355bcaf0e7ed96e3b63ed Mon Sep 17 00:00:00 2001
From: descoste <descoste@pc-bioinf01.embl.de>
Date: Thu, 21 Apr 2022 11:00:46 +0200
Subject: [PATCH] replace by main
---
.gitlab-ci.yml | 12 ++++++++---
.../bowtie2/Singularity.bowtie2-241cv1 | 1 +
.../mapping/bowtie2/Singularity.bowtie2-245 | 1 +
yaml-files/mapping/bowtie2-deploy.yaml | 20 +++++++++++++++++++
yaml-files/mapping/bowtie2-test.backup | 13 ++++++++++++
5 files changed, 44 insertions(+), 3 deletions(-)
create mode 100644 yaml-files/mapping/bowtie2-deploy.yaml
create mode 100644 yaml-files/mapping/bowtie2-test.backup
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 02fe539..2a46440 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -45,10 +45,16 @@ include:
- local: "yaml-files/image-analysis/deeplabcut-deploy.yaml"
#####################
-# Mapping
+# Quality control
#####################
include:
- local: "yaml-files/quality-control/fastqc-deploy.yaml"
- - local: "yaml-files/quality-control/bowtie2-deploy.yaml"
-
\ No newline at end of file
+
+
+#####################
+# Mapping
+#####################
+
+include:
+ - local: "yaml-files/mapping/bowtie2-deploy.yaml"
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 b/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
index 71bebf4..25e57fd 100644
--- a/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
+++ b/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
@@ -10,3 +10,4 @@ From: biocontainers/bowtie2:v2.4.1_cv1
%labels
Author Nicolas Descostes
+
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-245 b/recipes/mapping/bowtie2/Singularity.bowtie2-245
index 8b9822a..9af3331 100644
--- a/recipes/mapping/bowtie2/Singularity.bowtie2-245
+++ b/recipes/mapping/bowtie2/Singularity.bowtie2-245
@@ -10,3 +10,4 @@ From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
%labels
Author Nicolas Descostes
+
diff --git a/yaml-files/mapping/bowtie2-deploy.yaml b/yaml-files/mapping/bowtie2-deploy.yaml
new file mode 100644
index 0000000..22ca8be
--- /dev/null
+++ b/yaml-files/mapping/bowtie2-deploy.yaml
@@ -0,0 +1,20 @@
+bowtie2-245-builddeploy:
+ extends: .templateBuildDeploy
+ variables:
+ BASENAME: bowtie2
+ TAG: 245
+ RECIPE_PATH: recipes/mapping/bowtie2
+ only:
+ changes:
+ - recipes/mapping/bowtie2/Singularity.bowtie2-245
+
+bowtie2-241cv1-builddeploy:
+ extends: .templateBuildDeploy
+ variables:
+ BASENAME: bowtie2
+ TAG: 241cv1
+ RECIPE_PATH: recipes/mapping/bowtie2
+ only:
+ changes:
+ - recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
+
diff --git a/yaml-files/mapping/bowtie2-test.backup b/yaml-files/mapping/bowtie2-test.backup
new file mode 100644
index 0000000..688424a
--- /dev/null
+++ b/yaml-files/mapping/bowtie2-test.backup
@@ -0,0 +1,13 @@
+bowtie2-241cv1-test:
+ extends: .templateTest
+ variables:
+ BASENAME: bowtie2
+ TAG: 241cv1
+ RECIPE_PATH: recipes/quality-control/bowtie2
+
+bowtie2-245-test:
+ extends: .templateTest
+ variables:
+ BASENAME: bowtie2
+ TAG: 245
+ RECIPE_PATH: recipes/quality-control/bowtie2
--
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