From 3b404b90d27490fae85f4a1d2d278aac749166c7 Mon Sep 17 00:00:00 2001
From: Nicolas Descostes <nicolas.descostes@embl.it>
Date: Sat, 16 Apr 2022 08:46:30 +0000
Subject: [PATCH] Revert "Merge branch 'submission' into 'main'"
This reverts merge request !10
---
.gitlab-ci.yml | 2 +-
recipes/mapping/bowtie2/Singularity.bowtie2-241cv1 | 12 ------------
recipes/mapping/bowtie2/Singularity.bowtie2-245 | 12 ------------
yaml-files/quality-control/fastqc-test.backup | 6 +++---
4 files changed, 4 insertions(+), 28 deletions(-)
delete mode 100644 recipes/mapping/bowtie2/Singularity.bowtie2-241cv1
delete mode 100644 recipes/mapping/bowtie2/Singularity.bowtie2-245
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 85fc2f5..88585d2 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 71bebf4..0000000
--- 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 "$@"
-
-%post
- mkdir /cluster /work /tsd /projects
-
-%labels
- Author Nicolas Descostes
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-245 b/recipes/mapping/bowtie2/Singularity.bowtie2-245
deleted file mode 100644
index 8b9822a..0000000
--- a/recipes/mapping/bowtie2/Singularity.bowtie2-245
+++ /dev/null
@@ -1,12 +0,0 @@
-Bootstrap: docker
-From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
-
-%runscript
- echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5"
- exec /bin/bash "$@"
-
-%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 a287f61..e7ad88c 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/
--
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