From 5b1011f6089333529be4d8cad6307245b00441cd Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 4 Jun 2018 16:42:27 +0200
Subject: [PATCH] add publishDir
---
src/nf_modules/UrQt/urqt.nf | 2 ++
src/nf_modules/cutadapt/cutadapt.nf | 4 ++++
2 files changed, 6 insertions(+)
diff --git a/src/nf_modules/UrQt/urqt.nf b/src/nf_modules/UrQt/urqt.nf
index 87a3728..ece556a 100644
--- a/src/nf_modules/UrQt/urqt.nf
+++ b/src/nf_modules/UrQt/urqt.nf
@@ -21,6 +21,7 @@ Channel
process trimming {
tag "$pair_id"
cpus 4
+ publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
@@ -53,6 +54,7 @@ Channel
process trimming {
tag "$reads.baseName"
cpus 4
+ publishDir "results/fastq/trimming/", mode: 'copy'
input:
file reads from fastq_files
diff --git a/src/nf_modules/cutadapt/cutadapt.nf b/src/nf_modules/cutadapt/cutadapt.nf
index bebdf41..094f30b 100644
--- a/src/nf_modules/cutadapt/cutadapt.nf
+++ b/src/nf_modules/cutadapt/cutadapt.nf
@@ -21,6 +21,7 @@ Channel
process adaptor_removal {
tag "$pair_id"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
@@ -51,6 +52,7 @@ Channel
process adaptor_removal {
tag "$reads.baseName"
+ publishDir "results/fastq/adaptor_removal/", mode: 'copy'
input:
file reads from fastq_files
@@ -83,6 +85,7 @@ Channel
process trimming {
tag "$pair_id"
+ publishDir "results/fastq/trimming/", mode: 'copy'
input:
set pair_id, file(reads) from fastq_files
@@ -113,6 +116,7 @@ Channel
process trimming {
tag "$reads.baseName"
+ publishDir "results/fastq/trimming/", mode: 'copy'
input:
file reads from fastq_files
--
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