From 956fd73f32d7418e62e012113770fb69b9d30456 Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Mon, 6 Sep 2021 18:12:21 +0200
Subject: [PATCH] =?UTF-8?q?modif=20chipster.nf=20&=20bedtools/main.nf=20aj?=
 =?UTF-8?q?out=20des=20fonction=20de=20cr=C3=A9ation=20et=20sloping=20des?=
 =?UTF-8?q?=20bed=20files.=20Il=20manque=20encore=20la=20transformation=20?=
 =?UTF-8?q?des=20bed=20en=20BigWig.?=
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---
 src/chipster.nf                 | 35 +++++++++++++++++++----
 src/nf_modules/bedtools/main.nf | 50 +++++++++++++++++++++++++++++++++
 2 files changed, 79 insertions(+), 6 deletions(-)

diff --git a/src/chipster.nf b/src/chipster.nf
index 903711d2..61cf3041 100755
--- a/src/chipster.nf
+++ b/src/chipster.nf
@@ -13,24 +13,30 @@ nextflow.enable.dsl=2
  ****************************************************************
 */
 
-params.paired_end = true
+params.paired_end = false
 /* false for single end data, true for paired-end data
 
 @type: Boolean
 */
 
-params.fastq = "data/tinyTestDataset/fastq/*_{1,2}.fastq"
+params.fastq = "./data/tiny-delta-te-dataset/fastq_rnaseq/*.gz"
 /* Fastq files
 
 @type: Files
 */
 
-params.genome = "data/tinyTestDataset/reference.fasta"
+params.genome = "./data/tiny-delta-te-dataset/synth.fasta"
 /* A genome file
 
 @type: File
 */
 
+params.chrom_sizes = "./data/tiny-delta-te-dataset/chrom.sizes"
+/* samtools generated genome.sizes file: samtools faidx synth.fasta and cut -f 1,2 synth.fasta.fai > chrom.sizes
+
+@type: File
+*/
+
 // params.idx = ""
 /* already indexed reference genome ? enter path...
 
@@ -50,6 +56,8 @@ params.sort_bam_out = "$params.project/Bam_filtered_sorted/"
 params.index_bam_out = "$params.project/Bam_filt_sort_indexed/"
 params.bam_to_bigwig_out = "$params.project/BigWig/" 
 params.peak_calling_bg_out = "$params.project/Peak_calling/"
+params.bam_to_bed_out = "$params.project/Bed/"
+params.bed_slop_out = "$params.project/Bed_sloped/"
 
 /*
  ****************************************************************
@@ -59,6 +67,7 @@ params.peak_calling_bg_out = "$params.project/Peak_calling/"
 
 log.info "fastq files : ${params.fastq}"
 log.info "genome file : ${params.genome}"
+log.info "genome sizes : ${params.chrom_sizes}"
 /* log.info "indexed genome file : ${params.idxgenome}" */
 
 /*
@@ -99,7 +108,7 @@ Channel
   .fromPath( params.genome )
   .ifEmpty { error "Cannot find any files matching: ${params.genome}" }
   .map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
-  .set { genome_file } 
+  .set { genome_file }
 
 /* 
 Channel // IP & CTRL names
@@ -116,6 +125,12 @@ Channel
   .set { genome_idx }
 */
 
+Channel
+  .fromPath( params.chrom_sizes )
+  .ifEmpty { error "Cannot find any files matching: ${params.chrom_sizes}" }
+  .map{it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set{ genome_sizes }
+
 /*
  ****************************************************************
                           Imports
@@ -134,6 +149,8 @@ include { sort_bam } from "./nf_modules/samtools/main.nf"
 include { index_bam } from "./nf_modules/samtools/main.nf"
 include { bam_to_bigwig } from "./nf_modules/deeptools/main.nf"
 include { peak_calling_bg } from "./nf_modules/macs3/main.nf"
+include { bam_to_bed } from "./nf_modules/bedtools/main.nf"
+include { bed_slop } from "./nf_modules/bedtools/main.nf"
 
 /*
  ****************************************************************
@@ -179,10 +196,16 @@ workflow {
   sort_bam(filter_bam_quality.out.bam)
 
   // samtools_index
-  index_bam(sort_bam.out.bam)
+  // index_bam(sort_bam.out.bam.collect())
 
   // Create a bigwig file
-  bam_to_bigwig(index_bam.out.bam_idx)
+  // bam_to_bigwig(index_bam.out.bam_idx)
+
+  // From Bam to Bed
+  bam_to_bed(sort_bam.out.bam)
+
+  // Extension of reads with bedtools slop
+  bed_slop(bam_to_bed.out.bed, genome_sizes.collect())
 
   // peak calling using MACS3 Prend des bed ou des bam en entrée...
   // peak_calling_bg()
diff --git a/src/nf_modules/bedtools/main.nf b/src/nf_modules/bedtools/main.nf
index 9400abf4..6826615f 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -119,3 +119,53 @@ bedtools genomecov \
   -bg > ${bam.simpleName}.bg
 """
 }
+
+params.bam_to_bed = ""
+params.bam_to_bed_out = ""
+process bam_to_bed {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${bam_id}"
+  if (params.bam_to_bed_out != "") {
+    publishDir "results/${params.bam_to_bed_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(bam_id), path(bam)
+
+  output:
+  tuple val(bam_id), path("*.bed"), emit: bed
+
+  script:
+"""
+bedtools bamtobed \
+  -i ${bam} \
+  > ${bam.simpleName}.bed
+"""
+}
+
+params.bed_slop = ""
+params.bed_slop_out = ""
+process bed_slop {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${bed_id}"
+  if (params.bed_slop_out != "") {
+    publishDir "results/${params.bed_slop_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(bed_id), path(bed)
+  tuple val(file_id), path(chromsizes)
+
+  output:
+  tuple val(bed_id), path("*_sloped.bed"), emit: bed_sloped
+
+  script:
+"""
+bedtools slop -s -r 100 -l 0 \
+  -i ${bed} \
+  -g ${chromsizes} \
+  > ${bed.simpleName}_sloped.bed
+"""
+}
\ No newline at end of file
-- 
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