From b21b4aae4f627e368f3fe98287bc6557976dadbf Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Wed, 18 Oct 2023 13:39:14 +0200
Subject: [PATCH] add publishing directory for convert2bed files

---
 conf/modules.config | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 3e0afe44..9a218711 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -45,6 +45,14 @@ process {
         ]
     }
 
+    withName: CONVERT2BED {
+        publishDir = [
+            path: { "${params.genomes_base}/convert2bed" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
@@ -178,11 +186,6 @@ process {
         ext.when         = { !params.skip_qc && !params.fusioninspector_only && (params.starfusion || params.all)}
     }
 
-    withName: REFORMAT {
-        ext.args = "forcetrimright=75"
-        ext.args2 = "forcetrimleft=75"
-    }
-
     withName: SAMPLESHEET_CHECK {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },