From ffe94839a4c226a9fd0b3741caede9b2cb63fe8e Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 7 Nov 2019 14:20:04 -0600
Subject: [PATCH] Remove publish dirs for intermediate processes
---
workflow/main.nf | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index ec7db98..9d5a92d 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -36,7 +36,6 @@ references = params.references
process checkDesignFile {
tag "${name}"
- publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
module 'python/3.6.1-2-anaconda'
input:
@@ -63,7 +62,6 @@ process checkDesignFile {
process untarBCL {
tag "${tar}"
- publishDir "${outDir}/${task.process}", mode: 'copy'
module 'pigz/2.4'
input:
@@ -114,7 +112,7 @@ if (bclCount.value == 1) {
process countDesign {
tag "${name}"
- publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
+ publishDir "${outDir}/${task.process}/${name}", mode: 'copy'
input:
file fastqs from cellrangerCount.collect()
@@ -137,7 +135,6 @@ process fastqc {
tag "${bclName}"
queue 'super'
- publishDir "${outDir}/misc/${task.process}/${name}/${bclName}", mode: 'copy', pattern: "{*fastqc.zip}"
module 'fastqc/0.11.5:parallel'
input:
@@ -161,7 +158,6 @@ process fastqc {
process versions {
tag "${name}"
- publishDir "${outDir}/misc/${task.process}/${name}", mode: 'copy'
module 'python/3.6.1-2-anaconda:cellranger/3.1.0:bcl2fastq/2.19.1:fastqc/0.11.5:pandoc/2.7'
input:
--
GitLab