From 71b2d5f746b53ac6fa63bb45569bec4e8a2d97e9 Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Wed, 20 Dec 2023 18:10:15 +0100
Subject: [PATCH] Store UNTAR output in sample `data/` subdirectory

---
 conf/modules.config | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index 8ce91cf..eccef41 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -32,7 +32,15 @@ process {
         ]
     }
 
-    // store sample-specifc results in the per-sample subfolder
+    // Store sample-specific results in per-sample subfolders
+    withName: 'UNTAR_SPACERANGER_INPUT|UNTAR_DOWNSTREAM_INPUT' {
+        publishDir = [
+            path: { "${params.outdir}/${meta.id}/data/untar" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: FASTQC {
         publishDir = [
             path: { "${params.outdir}/${meta.id}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },