Commit e4b1822a authored by nlecouvr's avatar nlecouvr
Browse files

addition of the bowtie alignment

parent 33b8d389
nextflow.enable.dsl=2
/*========================= modules import ================================*/
include { fastp } from "./nf_modules/fastp/main.nf"
include { index_fasta, mapping_fastq } from "./nf_modules/bowtie2/main.nf"
include { fasta_from_bed } from "./nef_modules/bedtool/main"
params.fastq = "data/DamID/*_{1,2}.fastq"
log.info "fasta file : ${params.fasta}"
log.info "bed file : ${params.bed}"
channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.map { it -> [it.simpleName, it]}
.set { bed_files }
channel
channel
.fromFilePairs( params.fastq, size: -1)
.set { fastq_files }
/*================================ workflow ================================*/
workflow {
fastp(fastq_files)
fasta_from_bed(fasta_files, bed_files)
//mapping
index_fasta(fasta_from_bed.out)
mapping_fastq(index_fasta.out.out.index.collect(),
fastq_files)
}
\ No newline at end of file
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