From 69fe17d30184de5c282173aefa7d3e22b0fdd220 Mon Sep 17 00:00:00 2001
From: DLBPointon <damonlbp@hotmail.co.uk>
Date: Fri, 6 Dec 2024 09:14:41 +0000
Subject: [PATCH] Replace generate_csv singularity container

---
 modules/local/generate_cram_csv.nf | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/local/generate_cram_csv.nf b/modules/local/generate_cram_csv.nf
index f46c1ce..0085365 100755
--- a/modules/local/generate_cram_csv.nf
+++ b/modules/local/generate_cram_csv.nf
@@ -2,7 +2,9 @@ process GENERATE_CRAM_CSV {
     tag "${meta.id}"
     label 'process_single'
 
-    container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1'
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' :
+        'biocontainers/mulled-v2-1a6fe65bd6674daba65066aa796ed8f5e8b4687b:688e175eb0db54de17822ba7810cc9e20fa06dd5-0' }"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {