From 2b2b50b9492d788040fa098283bcc4b3ae1d0bc2 Mon Sep 17 00:00:00 2001
From: Xavier Grand <157-xgrand@users.noreply.gitbio.ens-lyon.fr>
Date: Mon, 25 Jul 2022 13:46:21 +0200
Subject: [PATCH] add STAR and HTseq to RNAseq_XGR.nf
---
src/RNAseq_XGR.nf | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index 50483da..2992340 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -76,6 +76,7 @@ params.star_index_out = "$params.project/STARindex/"
log.info "Annotation: ${params.gtf}"
log.info "Genome fasta file: ${params.fasta}"
+log.info "Genome index location: ${params.idx}"
/*
****************************************************************
@@ -104,6 +105,7 @@ include { multiqc } from './nf_modules/multiqc/main.nf' addParams(multiqc_out: "
include { fastp } from "./nf_modules/fastp/main.nf"
include { index_with_gtf } from "./nf_modules/star/main_2.7.8a.nf"
include { mapping_fastq } from "./nf_modules/star/main_2.7.8a.nf"
+include { mapping_withindex } from "./nf_modules/star/main_2.7.8a.nf"
include { htseq_count } from "./nf_modules/htseq/main.nf"
/*
@@ -150,7 +152,7 @@ workflow {
.fromPath( idx_genome )
.ifEmpty { error "Cannot find idexed genome reference files" }
.set { genome_indexed_input }
- mapping_fastq(genome_indexed_input, fastp.out.fastq)
+ mapping_withindex(genome_indexed_input, fastp.out.fastq)
}
//######################## HTseq COUNT #########################
--
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