Demmarage modif pour distance exon-pics FasterDB avec bedtools

src/CTCF2.yml

@@ -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:

src/MYCN.yml

@@ -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:

src/chipster.nf

@@ -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, )
 }
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src/nf_modules/bedtools/main.nf

@@ -195,3 +195,26 @@ bedtools genomecov -bg\
   > ${bed.simpleName}.bg
 """
 }
+
+params.nearestExonDist = ""
+params.nearestExonDist_out = ""
+process nearestExon_To_Peak {
+  container = "${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
+"""
+}
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