fix: merged bams will now preserve read groups, v->0.14.1

cschu · Oct 18, 2024 · 1d007a3 · 1d007a3
1 parent b65ad9e
commit 1d007a3
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/nevermore/modules/align/helpers.nf b/nevermore/modules/align/helpers.nf
@@ -16,7 +16,7 @@ process merge_and_sort {
 
     // need a better detection for this
     if (bamfiles instanceof Collection && bamfiles.size() >= 2) {
-        merge_cmd = "samtools merge -@ $task.cpus ${sort_order} bam/${sample.id}.bam ${bamfiles}"
+        merge_cmd = "samtools merge -c -@ $task.cpus ${sort_order} bam/${sample.id}.bam ${bamfiles}"
     } else {
         merge_cmd = "ln -s ../${bamfiles[0]} bam/${sample.id}.bam"
     }

diff --git a/nextflow.config b/nextflow.config
@@ -4,5 +4,5 @@ manifest {
 	description = "Metaomics pipeline toolbox"
 	name = "nevermore"
 	nextflowVersion = ">=22.10.6"
-	version = "0.14.0"
+	version = "0.14.1"
 }