From 7e301319fc611af046b1842e249aeee04fb7e4eb Mon Sep 17 00:00:00 2001
From: Natalia Garcia <natalia.garcia@nanoporetech.com>
Date: Wed, 27 May 2026 09:29:30 +0000
Subject: [PATCH] Use mode copy in publishDir [CW-7279]

---
 subworkflows/mods.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/mods.nf b/subworkflows/mods.nf
index 547c276..e00247e 100644
--- a/subworkflows/mods.nf
+++ b/subworkflows/mods.nf
@@ -44,7 +44,7 @@ process runModkitPileup {
         tuple val(alias),
             path("${alias}.mods.bedmethyl.gz"),
             emit: bedmethyl
-    publishDir "${params.out_dir}/${output_key}/mods"
+    publishDir "${params.out_dir}/${output_key}/mods", mode: 'copy'
 
     script:
     output_key = alias == "cohort" ? "cohort" : "samples/${alias}"  // nodef
@@ -77,7 +77,7 @@ process modkit_tobigwig {
         tuple val(alias),
             path("${alias}.mods.*.bw"),
             emit: bigwig
-    publishDir "${params.out_dir}/${output_key}/mods"
+    publishDir "${params.out_dir}/${output_key}/mods", mode: 'copy'
 
     script:
     output_key = alias == "cohort" ? "cohort" : "samples/${alias}"  // nodef
@@ -112,7 +112,7 @@ process summariseModkitBedmethyl {
         tuple val(alias),
             path("${alias}.mods.summary.tsv"),
             emit: summary
-    publishDir "${params.out_dir}/${output_key}/mods"
+    publishDir "${params.out_dir}/${output_key}/mods", mode: 'copy'
 
     script:
     output_key = alias == "cohort" ? "cohort" : "samples/${alias}"  // nodef