From 82ac6ea35811ca8b19d3b3be9616cfdd4c696a82 Mon Sep 17 00:00:00 2001
From: Emmanuel Labaronne <emmanuel.labaronne@ens-lyon.fr>
Date: Tue, 26 Jan 2021 09:02:35 +0100
Subject: [PATCH] src/RibosomeProfiling.nf : don't save intermediaire fastq
---
src/RibosomeProfiling.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/RibosomeProfiling.nf b/src/RibosomeProfiling.nf
index bb19b1c5..aad75c17 100644
--- a/src/RibosomeProfiling.nf
+++ b/src/RibosomeProfiling.nf
@@ -127,7 +127,7 @@ process fastqc_raw {
process trimming {
tag "$file_id"
- publishDir "${params.output}/01_cutadapt/", mode: 'copy'
+ //publishDir "${params.output}/01_cutadapt/", mode: 'copy'
echo true
input:
@@ -179,7 +179,7 @@ process fastqc_cut {
process rRNA_removal {
tag "$file_id"
- publishDir "${params.output}/02_rRNA_depletion/", mode: 'copy'
+ //publishDir "${params.output}/02_rRNA_depletion/", mode: 'copy'
input:
set file_id, file(reads) from CUTADAPT_OUTPUT_FILTER
@@ -660,7 +660,7 @@ process multiqc {
input:
// file ('fastqc/*') from OUTPUT_FASTQC_RAW.collect().ifEmpty([])
- file ('*') from CUTADAPT_LOG.collect().ifEmpty([])
+// file ('*') from CUTADAPT_LOG.collect().ifEmpty([])
file ('fastqc/*') from OUTPUT_FASTQC_CUT.collect().ifEmpty([])
file ('*') from FILTER_LOG.collect().ifEmpty([])
// file ('fastqc/*') from OUTPUT_FASTQC_FILTER.collect().ifEmpty([])
@@ -669,7 +669,7 @@ process multiqc {
file ('*') from HTSEQ_COUNT.collect().ifEmpty([])
file ('*') from POSTGENOME_LOG.collect().ifEmpty([])
// file ('fastqc/*') from OUTPUT_FASTQC_POSTGENOME.collect().ifEmpty([])
- file ('*') from RNASEQC_OUTPUT.collect().ifEmpty([])
+// file ('*') from RNASEQC_OUTPUT.collect().ifEmpty([])
output:
file "multiqc_report.html" into multiqc_report
--
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