Use Bioconda/BioContainers for bwa-mem2 module

nf-core · Mar 19, 2024 · 177bf69 · 177bf69
1 parent c7f1774
commit 177bf69
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Showing 3 changed files with 13 additions and 21 deletions.
diff --git a/modules/local/bwa-mem2/mem/Dockerfile b/modules/local/bwa-mem2/mem/Dockerfile
diff --git a/modules/local/bwa-mem2/mem/environment.yml b/modules/local/bwa-mem2/mem/environment.yml
@@ -0,0 +1,9 @@
+name: bwa-mem2_mem
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::bwa-mem2=2.2.1
+  - bioconda::samtools=1.19.2
+  - bioconda::sambamba=1.0
diff --git a/modules/local/bwa-mem2/mem/main.nf b/modules/local/bwa-mem2/mem/main.nf
@@ -2,8 +2,10 @@ process BWAMEM2_ALIGN {
     tag "${meta.id}"
     label 'process_high'
 
-    // TODO(SW): create BioContainers multi-package image when appropriate
-    container 'docker.io/scwatts/bwa-mem2:2.2.1'
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' :
+        'quay.io/biocontainers/mulled-v2-4dde50190ae599f2bb2027cb2c8763ea00fb5084:544519c4a0ff7e9616a3b44afde1f143c52f10c3-0' }"
 
     input:
     tuple val(meta), path(reads_fwd), path(reads_rev)