From 8e91baf69ace351f1de045dea870c8b53de9d6e2 Mon Sep 17 00:00:00 2001
From: Carine <carine.rey@ens-lyon.fr>
Date: Tue, 8 Mar 2022 15:45:06 +0100
Subject: [PATCH] change gff fro gtf
---
src/RNAseq_cec.nf | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/src/RNAseq_cec.nf b/src/RNAseq_cec.nf
index 2f19bcd..b0749f5 100644
--- a/src/RNAseq_cec.nf
+++ b/src/RNAseq_cec.nf
@@ -3,7 +3,8 @@ nextflow.enable.dsl=2
log.info "fastq files: ${params.fastq}"
log.info "fasta cds file: ${params.cds_fasta}"
log.info "fasta genomic file: ${params.genomic_fasta}"
-log.info "fasta gff3 file: ${params.genomic_gff3}"
+log.info "fasta gtf file: ${params.genomic_gtf}"
+
include { fastp } from './nf_modules/fastp/main.nf' addParams(fastp_out: "fastQC/")
include {
@@ -20,7 +21,7 @@ include {
)
include {
- index_with_gff as star_index_with_gff;
+ index_with_gtf as star_index_with_gtf;
mapping_fastq as star_mapping_fastq
} from './nf_modules/star/main.nf' addParams(
star_mapping_fastq_out: "star_bam/"
@@ -31,7 +32,7 @@ include { index_bam
htseq_out: "star_bam/"
)
-include { htseq_count_with_gff
+include { htseq_count as htseq_count_with_gtf
} from './nf_modules/htseq/main.nf' addParams(
htseq_out: "htseq_count/"
)
@@ -61,10 +62,10 @@ channel
.set { genomic_fasta_file }
channel
- .fromPath( params.genomic_gff3 )
- .ifEmpty { error "Cannot find any gff3 files matching: ${params.genomic_gff3}" }
+ .fromPath( params.genomic_gtf )
+ .ifEmpty { error "Cannot find any gtf files matching: ${params.genomic_gtf}" }
.map { it -> [it.simpleName, it]}
- .set { genome_gff3_file }
+ .set { genome_gtf_file }
workflow {
//trim data
@@ -82,7 +83,7 @@ workflow {
//star mapping
//// star index
- star_index_with_gff(genomic_fasta_file,genome_gff3_file)
+ star_index_with_gtf(genomic_fasta_file,genome_gtf_file)
star_index = star_index_with_gff.out
////star mapping
@@ -95,9 +96,9 @@ workflow {
//// index bam
index_bam(star_mapping_fastq.out.bam)
- htseq_count_with_gff(
+ htseq_count_with_gtf(
index_bam.out.bam_idx,
- genome_gff3_file
+ genome_gtf_file
)
//report multiqc
--
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