Merge branch 'submission' into 'main'

bowtie2

See merge request !11

.gitlab-ci.yml

@@ -36,6 +36,21 @@ image:
 
 ## WRITE YOUR TEST RULE HERE AFTER BRANCHING ON SUBMISSION AND CREATE A MERGE REQUEST
 
+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
+
+
 #####################
 # Image analysis
 #####################
@@ -44,7 +59,7 @@ include:
   - local: "yaml-files/image-analysis/deeplabcut-deploy.yaml"
 
 #####################
-## Quality control
+# Mapping
 #####################
 
 include:

recipes/mapping/bowtie2/Singularity.bowtie2-241cv1

+Bootstrap: docker
+From: biocontainers/bowtie2:v2.4.1_cv1
+
+%runscript
+    echo "Running container biocontainers/bowtie2:v2.4.1_cv1, Bowtie v2.4.1"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes

recipes/mapping/bowtie2/Singularity.bowtie2-245

+Bootstrap: docker
+From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
+
+%runscript
+    echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes

recipes/quality-control/bowtie2/Singularity.bowtie2-241cv1

+Bootstrap: docker
+From: biocontainers/bowtie2:v2.4.1_cv1
+
+%runscript
+    echo "Running container biocontainers/bowtie2:v2.4.1_cv1, Bowtie v2.4.1"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes

recipes/quality-control/bowtie2/Singularity.bowtie2-245

+Bootstrap: docker
+From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
+
+%runscript
+    echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes

yaml-files/quality-control/fastqc-test.backup

@@ -3,7 +3,7 @@ fastqc-0119cv7-test:
   variables:
     BASENAME: fastqc
     TAG: 0119cv7
-    RECIPE_PATH: recipes/quality-control/fastqc/
+    RECIPE_PATH: recipes/quality-control/fastqc
 
 
 fastqc-0119cv8-test:
@@ -11,11 +11,11 @@ fastqc-0119cv8-test:
   variables:
     BASENAME: fastqc
     TAG: 0119cv8
-    RECIPE_PATH: recipes/quality-control/fastqc/
+    RECIPE_PATH: recipes/quality-control/fastqc
 
 fastqc-0119cv6-test:
   extends: .templateTest
   variables:
     BASENAME: fastqc
     TAG: 0119cv6
-    RECIPE_PATH: recipes/quality-control/fastqc/
+    RECIPE_PATH: recipes/quality-control/fastqc