From b9f3d34888b93d7fe3d4a83c3d83912f7d9cdca3 Mon Sep 17 00:00:00 2001
From: mherbett <marion.herbette@ens-lyon.fr>
Date: Wed, 6 Jun 2018 14:40:49 +0000
Subject: [PATCH] RNASeq.nf : emove channel caion, and modiication of inpu fil
m cutadap
---
src/RNASeq.nf | 11 +----------
1 file changed, 1 insertion(+), 10 deletions(-)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index 244a734..8b03e38 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -49,22 +49,13 @@ process adaptor_removal {
* for paired-end data
*/
-params.fastq = "$baseDir/data/fastq/*_{1,2}.fastq"
-
-log.info "fastq files : ${params.fastq}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-
process trimming {
tag "${reads}"
cpus 4
publishDir "results/fastq/trimming/", mode: 'copy'
input:
- file reads from fastq_files
+ file reads from fastq_files_cut
output:
file "*_trim_R{1,2}.fastq.gz" into fastq_files_trim
--
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