Commit b6467be2 authored by Xavier Grand's avatar Xavier Grand
Browse files

Demmarage modif pour distance exon-pics FasterDB avec bedtools

parent b1bb6953
......@@ -25,6 +25,9 @@ idx: "/home/adminxavier/CTCF/Ref/genomeindex/"
# output folder under results/ directory
project: "CTCF_peak_calling_input_Genome_part2"
# FasterDB exons bed file
exons: "/home/adminxavier/CTCF/ChIPster/data/exon_sorted.bed"
input:
row1:
......
......@@ -25,6 +25,9 @@ idx: "/home/adminxavier/CTCF/Ref/genomeindex/"
# output folder under results/ directory
project: "SRA293647_MYCN_BE2"
# FasterDB exons bed file
exons: "/home/adminxavier/CTCF/ChIPster/data/exon_sorted.bed"
input:
row1:
......
......@@ -17,7 +17,8 @@ params.peak_calling_out = "$params.project/Peak_calling/"
params.bam_to_bed_out = "$params.project/Bed/"
params.bed_slop_out = "$params.project/Bed_sloped/"
params.bedGraph_out = "$params.project/BedGraph/"
params.chipseq_bam2BW_out = "$params.project/chipseq_BigWig"
params.chipseq_bam2BW_out = "$params.project/chipseq_BigWig/"
params.nearestExonDist_out = "$params.project/nearest_Exon_From_Peak/"
/*
****************************************************************
......@@ -28,6 +29,7 @@ params.chipseq_bam2BW_out = "$params.project/chipseq_BigWig"
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}"
/*
****************************************************************
......@@ -72,6 +74,11 @@ 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 }
/*
****************************************************************
Imports
......@@ -90,6 +97,7 @@ 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"
/*
****************************************************************
......@@ -162,6 +170,9 @@ workflow {
index_bam_chipster.out.bam_idx.groupTuple(by: 3).set { combined_bams }
combined_bams.map { it -> if(it[4][0] == 'IP') { [it[3], it[1][0], it[1][1]] } else {[ it[3], it[1][1], it[1][0]]} }.set { peak_calling_channel_in }
// peak calling using MACS3 Prend des bed ou des bam en entrée...
// peak calling using MACS3, bed or bam files as input...
peak_calling(peak_calling_channel_in)
// Nearest fasterDB exons detection and distance calculation.
// nearestExon_To_Peak(peak_calling.out.bed, )
}
\ No newline at end of file
......@@ -194,4 +194,27 @@ bedtools genomecov -bg\
-g ${chromsizes} \
> ${bed.simpleName}.bg
"""
}
params.nearestExonDist = ""
params.nearestExonDist_out = ""
process nearestExon_To_Peak {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bed_id}"
if (params.nearestExonDist_out != "") {
publishDir "results/${params.nearestExonDist_out}", mode: 'copy'
}
input:
tuple val(bed_id), path(bed), val(condition), val(type)
path( exons )
output:
tuple val(bed_id), path("*_nearestExon.bed"), val(condition), val(type), emit: bed_exon
script:
"""
bedtools closest -d -a ${bed} -b ${db} > ${bed_id}_nearestExon.bed
"""
}
\ No newline at end of file
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