Commit adc63251 authored by nlecouvr's avatar nlecouvr
Browse files

addition of fasta_from_bed

parent 9e1bd683
......@@ -2,8 +2,25 @@ nextflow.enable.dsl=2
include { fastp } from "./nf_modules/fastp/main.nf"
include { fasta_from_bed } from "./nef_modules/bedtools/main.nf"
params.fastq = "data/fastq/*_{1,2}.fastq"
log.info "fasta file : ${params.fasta}"
log info "bed file : ${params.bed}"
channel
.fromPath( params.fasta )
.ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
.map { it -> [it.simpleName, it]}
.set { fasta_files }
channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.map { it -> [it.simpleName, it]}
.set { bed_files }
channel
.fromFilePairs( params.fastq, size: -1)
.set { fastq_files }
......@@ -11,4 +28,5 @@ channel
workflow {
fastp(fastq_files)
fasta_from_bed(fasta_files, bed_files)
}
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