Merge branch 'dev' into dsl2-fix-sharding

nf-core · Feb 7, 2025 · 8b5a708 · 8b5a708
2 parents 81e213c + e5beb93
commit 8b5a708
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/subworkflows/local/map.nf b/subworkflows/local/map.nf
@@ -117,6 +117,11 @@ workflow MAP {
 
     // Only run merge lanes if we have more than one BAM to merge!
     ch_input_for_lane_merge = ch_mapped_lane_bam
+                                .toSortedList {
+                                    a, b ->
+                                    a[0]['lane'] <=> b[0]['lane'] ?: a[0]['colour_chemistry'] <=> b[0]['colour_chemistry'] ?: a[0]['shard_number'] <=> b[0]['shard_number']
+                                }
+                                .flatMap()
                                 .map {
                                     meta, bam ->
                                     new_meta = meta.clone().findAll{ it.key !in ['lane', 'colour_chemistry', 'shard_number'] }