Improve output sorting

nf-core · Mar 28, 2024 · d233d8f · d233d8f
1 parent 0da5870
commit d233d8f
Showing 1 changed file with 15 additions and 3 deletions.
diff --git 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