fix: switch file publish mode to copy for AWS compatibility

In the future we'd like to implement #21
CCBR · Aug 22, 2023 · 2eadd8e · 2eadd8e
1 parent 4574db3
commit 2eadd8e
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git 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
@@ -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)