From c915708057e3fc212b27abacac15b1178061696b Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Thu, 27 Apr 2023 16:09:12 +0200
Subject: [PATCH 1/2] save the star bam file

---
 conf/modules.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index a4602a9..5e3f1c2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -93,7 +93,8 @@ process {
             mode: 'copy',
             pattern: "*{bam,ReadsPerGene.out.tab,Log.final.out}",
             saveAs: { filename ->
-                if (filename ==~ /.*\.Log\.final\.out/ ) filename.concat('.txt')
+                filename.contains('.Log.final.out') ? filename.concat('.txt') :
+                filename
             }
         ]
     }

From 4a66996107317bb921a0cddd6701b9ad607f1858 Mon Sep 17 00:00:00 2001
From: Anders Jemt <jemten@users.noreply.github.com>
Date: Sat, 10 Jun 2023 15:13:02 +0100
Subject: [PATCH 2/2] upping fsatp time

---
 conf/hasta.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/hasta.config b/conf/hasta.config
index d2b5e60..b17f84e 100644
--- a/conf/hasta.config
+++ b/conf/hasta.config
@@ -14,7 +14,7 @@ process {
     withName:fastp {
         cpus = 8
         memory = "40GB"
-        time = "3h"
+        time = "6h"
     }
     withName:picard_collectrnaseqmetrics {
         memory = "10GB"