From 2e246cff1da2dd6e9e5376ffba58f0ef9f1b7488 Mon Sep 17 00:00:00 2001
From: Vincent Vanoosthuyse <vincent.vanoosthuyse@ens-lyon.fr>
Date: Mon, 23 Jul 2018 14:31:49 +0200
Subject: [PATCH] Add Bowtie 2 parameters to pipeline
---
src/RNAseq_sen1D.nf | 17 +----------------
1 file changed, 1 insertion(+), 16 deletions(-)
diff --git a/src/RNAseq_sen1D.nf b/src/RNAseq_sen1D.nf
index 99cbbd1..9906dd1 100644
--- a/src/RNAseq_sen1D.nf
+++ b/src/RNAseq_sen1D.nf
@@ -131,28 +131,13 @@ fi
* for paired-end data
*/
-params.fastq = "$baseDir/data/fastq/trimming/*_trim_{1,2}.fastq.gz"
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "fastq files : ${params.fastq}"
-log.info "index files : ${params.index}"
-
-Channel
- .fromFilePairs( params.fastq )
- .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
- .set { fastq_files }
-Channel
- .fromPath( params.index )
- .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
- .set { index_files }
-
process mapping_fastq {
tag "$pair_id"
cpus 4
publishDir "results/mapping/bams/", mode: 'copy'
input:
- set pair_id, file(reads) from fastq_files
+ set pair_id, file(reads) from fastq_files_trim
file index from index_files.toList()
output:
--
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