From 9800c42f19abbf4f68b3afb8da0d7d5a8b0d87da Mon Sep 17 00:00:00 2001
From: lgely <loic.gely@ens-lyon.fr>
Date: Thu, 23 Sep 2021 13:22:59 +0000
Subject: [PATCH] RNAseq.nf changed Kallisto "include" line to return results

---
 src/RNAseq_tp.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/RNAseq_tp.nf b/src/RNAseq_tp.nf
index abfb8ff0..95574aad 100644
--- a/src/RNAseq_tp.nf
+++ b/src/RNAseq_tp.nf
@@ -6,7 +6,7 @@ log.info "bed file : ${params.bed}"
 
 include { fastp } from "./nf_modules/fastp/main.nf"
 include { fasta_from_bed } from "./nf_modules/bedtools/main.nf"
-include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main.nf'
+include { index_fasta; mapping_fastq } from './nf_modules/kallisto/main.nf' addParams(mapping_fastq_out: "quantification/")
 
 params.fastq = "data/fastq/*_{1,2}.fastq"
 
-- 
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