From b3505f17eec33b4bf94867367704f9817eade81c Mon Sep 17 00:00:00 2001
From: elabaron <emmanuel.labaronne@ens-lyon.fr>
Date: Wed, 6 Jun 2018 15:14:14 +0000
Subject: [PATCH] RNAseq.nf: fix kallisto block
---
src/RNAseq.nf | 11 +----------
1 file changed, 1 insertion(+), 10 deletions(-)
diff --git a/src/RNAseq.nf b/src/RNAseq.nf
index f6353150..3d7ab45e 100644
--- a/src/RNAseq.nf
+++ b/src/RNAseq.nf
@@ -93,22 +93,13 @@ kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
"""
}
-params.index = "$baseDir/data/index/*.index.*"
-
-log.info "index files : ${params.index}"
-
-Channel
- .fromPath( params.index )
- .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
- .set { index_files }
-
process mapping_fastq {
tag "$reads"
cpus 4
publishDir "results/mapping/quantification/", mode: 'copy'
input:
- file reads from fastq_files
+ file reads from fastq_files_trim
file index from index_files.toList()
output:
--
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