From d233d8f4052208b4e572ddb1e8d561387df1cce5 Mon Sep 17 00:00:00 2001
From: Adrien Coulier <adrien.coulier@medsci.uu.se>
Date: Thu, 28 Mar 2024 16:56:51 +0100
Subject: [PATCH] Improve output sorting

---
 conf/modules.config | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 8b7a9c6..3b2fc02 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -42,13 +42,25 @@ process {
                             null
                             break
                         case ~/L\d+_multiqc_(report\.html|plots|data)/:
-                            "lanes/L${(filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def lane = (filename =~ /L(\d+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)L${lane}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "lanes/L${lane}/${new_filename}"
                             break
                         case ~/G-.+_multiqc_(report\.html|plots|data)/:
-                            "groups/G-${(filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def group = (filename =~ /G-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)G-${group}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "groups/${group}/${new_filename}"
                             break
                         case ~/D-.+_multiqc_(report\.html|plots|data)/:
-                            "rundirs/D-${(filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]}/${filename}"
+                            def rundir = (filename =~ /D-(.+)_multiqc_(report\.html|plots|data)/)[0][1]
+                            def new_filename = filename.replaceFirst(
+                                "(?<prefix>.*)D-${rundir}_(?<suffix>multiqc_(report\\.html|plots|data).*)",
+                                '${prefix}${suffix}')
+                            "rundirs/${rundir}/${new_filename}"
                             break
                         default:
                             filename