From 0e7efe2415c43910faac43b2c3855513617c648b Mon Sep 17 00:00:00 2001
From: fmalmeida <felipe.almeida.ext@boehringer-ingelheim.com>
Date: Mon, 11 Mar 2024 13:29:50 +0100
Subject: [PATCH] update publishDir path

---
 conf/modules.config | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 48446c3e..742019e2 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -216,7 +216,14 @@ if (params.aligner == 'kallisto') {
 if (params.aligner == 'cellrangermulti') {
     process {
         withName: FASTQC { ext.prefix = { "${meta.id}_${meta.feature_type}" } } // allow distinguishment of data types after renaming
-        withName: 'NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MULTI' { ext.prefix = null } // force it null, for some reason it was being wrongly read in the module
+        withName: 'NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_MULTI_ALIGN:CELLRANGER_MULTI' {
+            ext.prefix = null // force it null, for some reason it was being wrongly read in the module
+            publishDir = [
+                path: "${params.outdir}/${params.aligner}/count",
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
         withName: 'GUNZIP*' {
             publishDir = [
                 enabled: false
@@ -235,6 +242,12 @@ if (params.aligner == 'cellrangermulti') {
                 mode: params.publish_dir_mode
             ]
         }
+        withName: CELLRANGER_MKVDJREF {
+            publishDir = [
+                path: "${params.outdir}/${params.aligner}/mkvdjref",
+                mode: params.publish_dir_mode
+            ]
+        }
     }
 }