diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 85fc2f5a8f99b9f6d95060c77cea37e8d98200a6..88585d20280ec493b45091fc06a48e3161fae807 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -44,7 +44,7 @@ include: - local: "yaml-files/image-analysis/deeplabcut-deploy.yaml" ##################### -# Mapping +## Quality control ##################### include: diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 b/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 deleted file mode 100644 index 71bebf47885c86955456560947321137f20e2ba2..0000000000000000000000000000000000000000 --- a/recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 +++ /dev/null @@ -1,12 +0,0 @@ -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 "$@" - -%post - mkdir /cluster /work /tsd /projects - -%labels - Author Nicolas Descostes diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-245 b/recipes/mapping/bowtie2/Singularity.bowtie2-245 deleted file mode 100644 index 8b9822a8605f0a4ed98b10ee4e37903c2937f264..0000000000000000000000000000000000000000 --- a/recipes/mapping/bowtie2/Singularity.bowtie2-245 +++ /dev/null @@ -1,12 +0,0 @@ -Bootstrap: docker -From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2 - -%runscript - echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5" - exec /bin/bash "$@" - -%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 a287f61b269869fc713ee116cc8881e2c5cdba27..e7ad88ca552cd5344e2b4c3f21063e4c680fbb9c 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/