From 2c9527972ed58cfa3a88f68709ef8fd140faff85 Mon Sep 17 00:00:00 2001
From: "J. Christian Heide" <christian_heide@eva.mpg.de>
Date: Tue, 4 Feb 2025 17:04:31 +0100
Subject: [PATCH] Make order of `lane`, `colour_chemistry`, and `shard_number`
 consistent

---
 subworkflows/local/map.nf | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/subworkflows/local/map.nf b/subworkflows/local/map.nf
index cbd4e20f9..bb2dc0676 100644
--- a/subworkflows/local/map.nf
+++ b/subworkflows/local/map.nf
@@ -133,6 +133,11 @@ 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'] }