Commit 2e45e8d5 authored by nlecouvr's avatar nlecouvr
Browse files

global corrections

parent e4b1822a
......@@ -9,30 +9,37 @@ 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"
params.reads = "data/DamID/reads/*_{1,2}.fastq"
params.genome = "data/DamID/genome/*_{1,2}.fasta"
log.info "fastq files: ${params.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
.fromFilePairs( params.fastq, size: -1)
.set { fastq_files }
.fromPath( params.reads, chekIfExists: true)
.set {reads}
/*================================ workflow ================================*/
workflow {
fastp(fastq_files)
fasta_from_bed(fasta_files, bed_files)
fastp(reads)
//mapping
index_fasta(fasta_from_bed.out)
index_fasta(fasta)
mapping_fastq(index_fasta.out.out.index.collect(),
fastq_files)
reads)
workflow.onComplete {
println ( workflow.success "Au moins ça a pas planté, mais ça a surement pas marché quand même" )
}
}
\ No newline at end of file
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