From 1c82c3566ac5d32410853e269376fc208c66995c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Wed, 6 Jun 2018 10:57:26 +0200
Subject: [PATCH] Kallisto.nf: fix paired name
---
src/nf_modules/Kallisto/kallisto.nf | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/nf_modules/Kallisto/kallisto.nf b/src/nf_modules/Kallisto/kallisto.nf
index 0af1fc8..aa92350 100644
--- a/src/nf_modules/Kallisto/kallisto.nf
+++ b/src/nf_modules/Kallisto/kallisto.nf
@@ -54,12 +54,12 @@ Channel
.set { index_files }
process mapping_fastq {
- tag "$pair_id"
+ tag "$reads"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
- set pair_id, file(reads) from fastq_files
+ file reads from fastq_files
file index from index_files.toList()
output:
@@ -67,9 +67,9 @@ process mapping_fastq {
script:
"""
-mkdir ${pair_id}
+mkdir ${reads[0].baseName}
kallisto quant -i ${index} -t ${task.cpus} \
---bias --bootstrap-samples 100 -o ${pair_id} \
+--bias --bootstrap-samples 100 -o ${reads[0].baseName} \
${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
"""
}
--
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