Commit a44e9826 authored by nlecouvr's avatar nlecouvr
Browse files

functionnal version of the pipeline

parent 948ad068
......@@ -11,43 +11,33 @@ nextflow.enable.dsl=2
include { fastp } from "./nf_modules/fastp/main.nf"
include { index_fasta; mapping_fastq } from "./nf_modules/bowtie2/main.nf"
include { index_fasta; mapping_fastq } from "./nf_modules/bowtie2/main.nf" addParams(mapping_fastq_out: "mapping/")
params.genome = "data/genome/dm6.fasta"
params.reads = "data/reads/data.fastq"
params.fasta = "data/genome/*_G.fasta"
params.fastq = "data/reads/*_R.fastq"
params.help = false
log.info "reads files : ${params.reads}"
log.info "genome file : ${params.genome}"
channel
.fromPath("data/genome/dm6.fasta")
.set {genome}
/*
channel
.fromPath( params.bed )
.ifEmpty { error "Cannot find any bed files matching: ${params.bed}" }
.fromPath(params.fasta)
.ifEmpty { error "Cannot find any fasta files matching: ${params.genome}" }
.map { it -> [it.simpleName, it]}
.set { bed_files }
*/
.set {fasta_files}
channel
.fromFilePairs( "data/reads/data.fastq", size: -1 )
.set {reads}
.fromFilePairs(params.fastq, size: -1)
.set {fastq_files}
/*================================ workflow ================================*/
workflow {
fastp(reads)
fastp(fastq_files)
//mapping
index_fasta(genome)
index_fasta(fasta_files)
mapping_fastq(index_fasta.out.index.collect(),
fastp.out.fastq)
}
......
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