From af12435fa5e3adf240d48bf9f764a063c62593b8 Mon Sep 17 00:00:00 2001
From: "Moritz E. Beber" <midnighter@posteo.net>
Date: Tue, 5 Apr 2022 12:16:26 +0200
Subject: [PATCH] fix: use parameter for publish mode everywhere

---
 conf/modules.config | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 22db8d0..a910b8e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -43,7 +43,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
         publishDir = [
             path: { "${params.outdir}/fastqc/raw" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.html'
         ]
     }
@@ -53,7 +53,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
         publishDir = [
             path: { "${params.outdir}/fastqc/processed" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.html'
         ]
     }
@@ -69,7 +69,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/fastp" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.fastq.gz'
         ]
     }
@@ -88,7 +88,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/fastp" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.fastq.gz'
         ]
     }
@@ -104,7 +104,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/adapterremoval" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.fastq.gz'
         ]
     }
@@ -123,7 +123,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/adapterremoval" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.fastq.gz'
         ]
     }
@@ -132,7 +132,7 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             path: { "${params.outdir}/porechop" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.fastq.gz'
         ]
     }
@@ -169,7 +169,7 @@ process {
         ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/malt/${meta.db_name}" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.{rma6,tab,text,sam,log}'
         ]
     }
@@ -179,7 +179,7 @@ process {
         ext.prefix = { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}" },
-            mode: 'copy',
+            mode: params.publish_dir_mode,
             pattern: '*.{fastq.gz,txt}'
         ]
     }