From 145e79cd79e1cc0d64ba5ecba07fa2c14653bea4 Mon Sep 17 00:00:00 2001
From: Xavier Grand <157-xgrand@users.noreply.gitbio.ens-lyon.fr>
Date: Wed, 27 Jul 2022 14:59:58 +0200
Subject: [PATCH] Modif RNAseq_XGR.nf Add Samtools filters
---
src/RNAseq_XGR.nf | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/src/RNAseq_XGR.nf b/src/RNAseq_XGR.nf
index a5f8ff5..b336891 100644
--- a/src/RNAseq_XGR.nf
+++ b/src/RNAseq_XGR.nf
@@ -64,7 +64,7 @@ params.fastq = "${project}/fastq/*_{1,2}.fq.gz"
params.gtf = ""
params.fasta = ""
params.idx = ""
-params.filter_bam = "-F 268 -f 1 -q 10"
+params.filter_bam_mapped = "-F 268 -f 1 -q 10"
params.fastp_out = "$params.project/fastp/"
params.star_mapping_fastq_out = "$params.project/STAR/"
@@ -109,7 +109,8 @@ include { index_with_gtf } from "./nf_modules/star/main_2.7.8a.nf"
include { mapping_fastq } from "./nf_modules/star/main_2.7.8a.nf"
include { mapping_withindex } from "./nf_modules/star/main_2.7.8a.nf"
include { htseq_count } from "./nf_modules/htseq/main.nf"
-include { filter_bam } from "./nf_modules/samtools/main.nf"
+
+include { filter_bam_mapped } from "./nf_modules/samtools/main.nf"
include { stats_bam } from "./nf_modules/samtools/main.nf"
include { sort_bam } from "./nf_modules/samtools/main.nf"
include { index_bam } from "./nf_modules/samtools/main.nf"
@@ -137,7 +138,7 @@ workflow {
index_with_gtf(genome_file, gtf_file.collect())
mapping_fastq(index_with_gtf.out.index.collect(), fastp.out.fastq)
-
+ filter_bam_mapped(mapping_fastq.out.bam)
}
else {
idx_genome = "${params.idx}"
@@ -146,10 +147,13 @@ workflow {
.set { genome_indexed_input }
genome_indexed_input.view()
mapping_withindex(genome_indexed_input.collect(), fastp.out.fastq)
- htseq_count(mapping_withindex.out.bam, gtf_file)
+ stats_bam(mapping_withindex.out.bam)
+ filter_bam_mapped(mapping_withindex.out.bam)
}
- htseq_count(mapping_fastq.out.bam, gtf_file)
+ sort_bam(filter_bam_mapped.out.bam)
+ index_bam(sort_bam_mapped.out.bam)
+ htseq_count(sort_bam_mapped.out.bam, gtf_file)
//########################## QUALITY CHECKS ###################
--
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