From 7225543424b3da9dded141820498f282a99208de Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Wed, 3 Jan 2024 11:30:02 +0100
Subject: [PATCH] Re-order module config for clarify

---
 conf/modules.config | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 028c4cd..cbf2a7b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -32,21 +32,21 @@ process {
         ]
     }
 
-    // Store sample-specific results in per-sample subdirectories
-    withName: 'UNTAR_SPACERANGER_INPUT|UNTAR_DOWNSTREAM_INPUT' {
+    // Optionally save extracted Space Ranger reference archive
+    withName: 'SPACERANGER_UNTAR_REFERENCE' {
         publishDir = [
-            enabled: params.save_untar_output,
-            path: { "${params.outdir}/${meta.id}/data/untar" },
+            enabled: params.spaceranger_save_reference,
+            path: { "${params.outdir}/reference" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    // Optionally save extracted Space Ranger reference archive
-    withName: 'SPACERANGER_UNTAR_REFERENCE' {
+    // Store sample-specific results in per-sample subdirectories
+    withName: 'UNTAR_SPACERANGER_INPUT|UNTAR_DOWNSTREAM_INPUT' {
         publishDir = [
-            enabled: params.spaceranger_save_reference,
-            path: { "${params.outdir}/reference" },
+            enabled: params.save_untar_output,
+            path: { "${params.outdir}/${meta.id}/data/untar" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -70,7 +70,6 @@ process {
         ]
     }
 
-    // Store reports in sample-specific subdirectories
     withName: 'ST_READ_DATA|ST_QC_AND_NORMALISATION|ST_CLUSTERING|ST_SPATIAL_DE' {
         publishDir = [
             [