From 5a252dbe2f59a836985ec24faacf00dab738a3e8 Mon Sep 17 00:00:00 2001
From: Nathan Lecouvreur <nathan.lecouvreur@ens-lyon.fr>
Date: Wed, 19 Jan 2022 11:52:32 +0100
Subject: [PATCH] adding kalisto
---
src/RNASeq.nf | 3 +++
1 file changed, 3 insertions(+)
diff --git a/src/RNASeq.nf b/src/RNASeq.nf
index 1d7cc82..bb0803d 100644
--- a/src/RNASeq.nf
+++ b/src/RNASeq.nf
@@ -3,6 +3,7 @@ nextflow.enable.dsl=2
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"
@@ -29,4 +30,6 @@ 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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