From c56354c10b7b9f16b35893a572d1b720cc56832b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 18 Jan 2020 15:36:36 -0600
Subject: [PATCH] Set publishData mode to copy
---
workflow/rna-seq.nf | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 58590dd..8c4f6ae 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -15,7 +15,6 @@ deriva = Channel
bdbag = Channel
.fromPath(params.bdbag)
.ifEmpty { exit 1, "deriva cookie file for bdbag not found: ${params.bdbag}" }
-
repRID = params.repRID
outDir = params.outDir
@@ -30,7 +29,7 @@ derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
process getBag {
executor 'local'
tag "${repRID}"
- publishDir "${logsDir}/getBag", mode: 'symlink', pattern: "${repRID}.getBag.err"
+ publishDir "${logsDir}/getBag", mode: 'copy', pattern: "${repRID}.getBag.err"
input:
path credential, stageAs: 'credential.json' from deriva
@@ -56,7 +55,7 @@ process getBag {
*/
process getData {
tag "${repRID}"
- publishDir "${logsDir}/getData", mode: 'symlink', pattern: "${repRID}.getData.err"
+ publishDir "${logsDir}/getData", mode: 'copy', pattern: "${repRID}.getData.err"
input:
executor 'local'
@@ -92,7 +91,7 @@ process getData {
*/
process trimData {
tag "${repRID}"
- publishDir "${logsDir}/trimData", mode: 'symlink', pattern: "\${repRID}.trimData.*"
+ publishDir "${logsDir}/trimData", mode: 'copy', pattern: "\${repRID}.trimData.*"
input:
file(fastq) from fastqs
--
GitLab