Commit f75fe4fd authored by Xavier Grand's avatar Xavier Grand
Browse files

Fonctionnel

parent b6467be2
......@@ -18,7 +18,7 @@ params.bam_to_bed_out = "$params.project/Bed/"
params.bed_slop_out = "$params.project/Bed_sloped/"
params.bedGraph_out = "$params.project/BedGraph/"
params.chipseq_bam2BW_out = "$params.project/chipseq_BigWig/"
params.nearestExonDist_out = "$params.project/nearest_Exon_From_Peak/"
// params.nearestExonDist_out = "$params.project/nearest_Exon_From_Peak/"
/*
****************************************************************
......@@ -29,7 +29,7 @@ params.nearestExonDist_out = "$params.project/nearest_Exon_From_Peak/"
log.info "fastq folder : ${params.fastq_folder}"
log.info "genome file : ${params.genome}"
log.info "genome sizes : ${params.chrom_sizes}"
log.info "fasterDB exons bed file : ${params.exons}"
// log.info "fasterDB exons bed file : ${params.exons}"
/*
****************************************************************
......@@ -74,10 +74,13 @@ Channel
.map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set{ genome_sizes }
/*
Channel
.fromPath( params.exons )
.ifEmpty { error "Cannot find any files matching: ${params.exons }" }
.set { exons }
.map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { exonsDB }
*/
/*
****************************************************************
......@@ -97,7 +100,7 @@ include { sort_bam_chipster } from "./nf_modules/samtools/main.nf"
include { index_bam_chipster } from "./nf_modules/samtools/main.nf"
include { chipseq_bam2BW_chipster } from "./nf_modules/deeptools/main.nf"
include { peak_calling } from "./nf_modules/macs3/main.nf"
include { nearestExon_To_Peak } from "./nf_modules/bedtools/main.nf"
// include { nearestExon_To_Peak } from "./nf_modules/bedtools/main.nf"
/*
****************************************************************
......@@ -174,5 +177,5 @@ workflow {
peak_calling(peak_calling_channel_in)
// Nearest fasterDB exons detection and distance calculation.
// nearestExon_To_Peak(peak_calling.out.bed, )
// nearestExon_To_Peak(peak_calling.out.bed, exonsDB)
}
\ No newline at end of file
......@@ -215,6 +215,6 @@ process nearestExon_To_Peak {
script:
"""
bedtools closest -d -a ${bed} -b ${db} > ${bed_id}_nearestExon.bed
bedtools closest -d -a ${bed} -b ${exons} > ${bed_id}_nearestExon.bed
"""
}
\ No newline at end of file
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