Commit 145e79cd authored by Xavier Grand's avatar Xavier Grand
Browse files

Modif RNAseq_XGR.nf Add Samtools filters

parent 36a3562c
......@@ -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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