From b9c47ee767eae13fa6f44915dcdd14f4544bbc93 Mon Sep 17 00:00:00 2001
From: lgely <loic.gely@ens-lyon.fr>
Date: Thu, 23 Sep 2021 13:18:29 +0000
Subject: [PATCH] RNAseq_tp.nf implemented Kallisto
---
src/RNAseq_tp.nf | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/RNAseq_tp.nf b/src/RNAseq_tp.nf
index aaa25165..abfb8ff0 100644
--- a/src/RNAseq_tp.nf
+++ b/src/RNAseq_tp.nf
@@ -6,6 +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'
params.fastq = "data/fastq/*_{1,2}.fastq"
@@ -24,4 +25,6 @@ channel
workflow {
fastp(fastq_files)
fasta_from_bed(fasta_files, bed_files)
+ index_fasta(fasta_from_bed.out.fasta)
+ mapping_fastq(index_fasta.out.index.collect(), fastp.out.fastq)
}
--
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