From 2eadd8edcc23fda79055bde1d5ce1d52ab089c8e Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Tue, 22 Aug 2023 09:56:14 -0400
Subject: [PATCH] fix: switch file publish mode to copy for AWS compatibility

In the future we'd like to implement #21
---
 src/champagne/workflow/modules/local/qc.nf   | 2 +-
 src/champagne/workflow/modules/local/trim.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/champagne/workflow/modules/local/qc.nf b/src/champagne/workflow/modules/local/qc.nf
index 01b74599..3e84c751 100644
--- a/src/champagne/workflow/modules/local/qc.nf
+++ b/src/champagne/workflow/modules/local/qc.nf
@@ -1,7 +1,7 @@
 
 process FASTQC {
     tag { sample_id }
-    publishDir "$params.outdir/$sample_id/qc/", mode: 'symlink'
+    publishDir "$params.outdir/$sample_id/qc/", mode: 'copy'
 
     input:
         tuple val(sample_id), path(fastq)
diff --git a/src/champagne/workflow/modules/local/trim.nf b/src/champagne/workflow/modules/local/trim.nf
index ebf9f6db..1f06c0c5 100644
--- a/src/champagne/workflow/modules/local/trim.nf
+++ b/src/champagne/workflow/modules/local/trim.nf
@@ -2,7 +2,7 @@
 // https://github.com/nf-core/ampliseq/blob/dev/subworkflows/local/cutadapt_workflow.nf
 process TRIM_SE {
   tag { sample_id }
-  publishDir "$params.outdir/$sample_id", mode: 'symlink'
+  publishDir "$params.outdir/$sample_id", mode: 'copy'
 
   input:
     tuple val(sample_id), path(fastq)