diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 88585d20280ec493b45091fc06a48e3161fae807..ff6ea7554dc9b6154fa0fe70164fb201d23228e3 100644
--- a/.gitlab-ci.yml
+++ b/.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:
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 b/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
new file mode 100644
index 0000000000000000000000000000000000000000..71bebf47885c86955456560947321137f20e2ba2
--- /dev/null
+++ b/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
@@ -0,0 +1,12 @@
+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 "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-245 b/recipes/mapping/bowtie2/Singularity.bowtie2-245
new file mode 100644
index 0000000000000000000000000000000000000000..8b9822a8605f0a4ed98b10ee4e37903c2937f264
--- /dev/null
+++ b/recipes/mapping/bowtie2/Singularity.bowtie2-245
@@ -0,0 +1,12 @@
+Bootstrap: docker
+From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
+
+%runscript
+    echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes
diff --git a/recipes/quality-control/bowtie2/Singularity.bowtie2-241cv1 b/recipes/quality-control/bowtie2/Singularity.bowtie2-241cv1
new file mode 100644
index 0000000000000000000000000000000000000000..71bebf47885c86955456560947321137f20e2ba2
--- /dev/null
+++ b/recipes/quality-control/bowtie2/Singularity.bowtie2-241cv1
@@ -0,0 +1,12 @@
+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 "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes
diff --git a/recipes/quality-control/bowtie2/Singularity.bowtie2-245 b/recipes/quality-control/bowtie2/Singularity.bowtie2-245
new file mode 100644
index 0000000000000000000000000000000000000000..16bfa98f757badc9bd5a0fc7b92f393564ca1f6c
--- /dev/null
+++ b/recipes/quality-control/bowtie2/Singularity.bowtie2-245
@@ -0,0 +1,12 @@
+Bootstrap: docker
+From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
+
+%runscript
+    echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5"
+    exec /bin/bash "$@"
+
+%post
+    mkdir /cluster /work /tsd /projects
+
+%labels
+    Author Nicolas Descostes
diff --git a/yaml-files/quality-control/fastqc-test.backup b/yaml-files/quality-control/fastqc-test.backup
index e7ad88ca552cd5344e2b4c3f21063e4c680fbb9c..a287f61b269869fc713ee116cc8881e2c5cdba27 100644
--- a/yaml-files/quality-control/fastqc-test.backup
+++ b/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