From 26bd1d09438f44f4177585888530982de234d698 Mon Sep 17 00:00:00 2001
From: "Huska, Matthew" <HuskaM@rki.de>
Date: Wed, 13 Dec 2023 12:20:52 +0100
Subject: [PATCH] Update fastq_from_bam to publish illumina data properly.
 Regexes are geting crazy, need to rethink this.

---
 modules/alignment_processing.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/alignment_processing.nf b/modules/alignment_processing.nf
index 0f908f7..ca3b693 100644
--- a/modules/alignment_processing.nf
+++ b/modules/alignment_processing.nf
@@ -152,6 +152,8 @@ process fastq_from_bam {
             fn.matches('.*.mapped_merged.fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_merged(.fast[aq].gz)$', '$1') :
             fn.matches('.*.unmapped_merged_merged.fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_merged_merged(.fast[aq].gz)$', '$1') :
             fn.matches('.*.soft-clipped_merged.fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.soft-clipped_merged(.fast[aq].gz)$', '$1') :
+            fn.matches('.*.unmapped_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
+            fn.matches('.*.mapped_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') :
             fn
       }
     )