From f0d25e3c561c489e89f08a72be38f31b7ccd9651 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 18 Jan 2020 15:38:27 -0600
Subject: [PATCH] Remove sub-folders from logsDir
---
workflow/rna-seq.nf | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 8c4f6ae..bbb5a76 100755
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -29,7 +29,7 @@ derivaConfig = Channel.fromPath("${baseDir}/conf/replicate_export_config.json")
process getBag {
executor 'local'
tag "${repRID}"
- publishDir "${logsDir}/getBag", mode: 'copy', pattern: "${repRID}.getBag.err"
+ publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.getBag.err"
input:
path credential, stageAs: 'credential.json' from deriva
@@ -55,7 +55,7 @@ process getBag {
*/
process getData {
tag "${repRID}"
- publishDir "${logsDir}/getData", mode: 'copy', pattern: "${repRID}.getData.err"
+ publishDir "${logsDir}", mode: 'copy', pattern: "${repRID}.getData.err"
input:
executor 'local'
@@ -91,7 +91,7 @@ process getData {
*/
process trimData {
tag "${repRID}"
- publishDir "${logsDir}/trimData", mode: 'copy', pattern: "\${repRID}.trimData.*"
+ publishDir "${logsDir}", mode: 'copy', pattern: "\${repRID}.trimData.*"
input:
file(fastq) from fastqs
--
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