From aee27463cd159d14d3c9c37fae1d61d8b8a8badd Mon Sep 17 00:00:00 2001
From: xgrand <xavier.grand@ens-lyon.fr>
Date: Thu, 9 Sep 2021 12:38:21 +0200
Subject: [PATCH] =?UTF-8?q?modif=20pipeline=20bamcoverage=20deeptools=20po?=
=?UTF-8?q?ur=20chipseq=20et=20param=C3=A8tres?=
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---
src/chipster.nf | 20 ++++++++++++++++----
src/nf_modules/bedtools/main.nf | 26 ++++++++++++++++++++++++++
src/nf_modules/deeptools/main.nf | 27 +++++++++++++++++++++++++++
3 files changed, 69 insertions(+), 4 deletions(-)
diff --git a/src/chipster.nf b/src/chipster.nf
index 61cf3041..4af93862 100755
--- a/src/chipster.nf
+++ b/src/chipster.nf
@@ -58,6 +58,8 @@ 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/"
+params.bedGraph_out = "$params.project/BedGraph/"
+params.chipseq_bam2BG_out = "$params.project/chipseq_BigGig"
/*
****************************************************************
@@ -148,9 +150,11 @@ include { filter_bam_quality } from "./nf_modules/samtools/main.nf"
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 { chipseq_bam2BG } 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"
+include { bed_to_bedGraph } from "./nf_modules/bedtools/main.nf"
/*
****************************************************************
@@ -159,11 +163,12 @@ include { bed_slop } from "./nf_modules/bedtools/main.nf"
*/
workflow {
- // fastq_files.view() // Pour voir les fichier qui sont chargés
// fastp
fastp_default(fastq_files)
+
+ /*
// fastqc_rawdata
fastqc_raw(fastq_files)
// fastqc_processed
@@ -175,6 +180,7 @@ workflow {
fastqc_preprocessed.out.report
).collect()
)
+ */
// index reference genome
index_fasta(genome_file)
@@ -196,16 +202,22 @@ workflow {
sort_bam(filter_bam_quality.out.bam)
// samtools_index
- // index_bam(sort_bam.out.bam.collect())
+ index_bam(sort_bam.out.bam)
// Create a bigwig file
// bam_to_bigwig(index_bam.out.bam_idx)
+ // Chipseq Bam 2 bigwig file with reads extends
+ chipseq_bam2BG(index_bam.out.bam_idx)
+
// From Bam to Bed
- bam_to_bed(sort_bam.out.bam)
+ // bam_to_bed(sort_bam.out.bam)
// Extension of reads with bedtools slop
- bed_slop(bam_to_bed.out.bed, genome_sizes.collect())
+ // bed_slop(bam_to_bed.out.bed, genome_sizes.collect())
+
+ // From bed to bedgraph
+ // bed_to_bedGraph(bed_slop.out, 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 6826615f..bc017708 100644
--- a/src/nf_modules/bedtools/main.nf
+++ b/src/nf_modules/bedtools/main.nf
@@ -168,4 +168,30 @@ bedtools slop -s -r 100 -l 0 \
-g ${chromsizes} \
> ${bed.simpleName}_sloped.bed
"""
+}
+
+params.bedGraph = ""
+params.bedGraph_out = ""
+process bed_to_bedGraph {
+ container = "${container_url}"
+ label "big_mem_mono_cpus"
+ tag "${bed_id}"
+ if (params.bedGraph_out != "") {
+ publishDir "results/${params.bedGraph_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(bed_id), path(bed)
+ tuple val(file_id), path(chromsizes)
+
+ output:
+ tuple val(bed_id), path("*.bg"), emit: bedGraph
+
+ script:
+"""
+bedtools genomecov -bg\
+ -i ${bed} \
+ -g ${chromsizes} \
+ > ${bed.simpleName}.bg
+"""
}
\ No newline at end of file
diff --git a/src/nf_modules/deeptools/main.nf b/src/nf_modules/deeptools/main.nf
index 25468706..8a4b7932 100644
--- a/src/nf_modules/deeptools/main.nf
+++ b/src/nf_modules/deeptools/main.nf
@@ -104,3 +104,30 @@ plotProfile -m ${matrix} \
--plotTitle "${params.title}"
"""
}
+
+params.chipseq_bam2BG = ""
+params.chipseq_bam2BG_out = ""
+process chipseq_bam2BG {
+ container = "${container_url}"
+ label "big_mem_multi_cpus"
+ tag "$file_id"
+ if (params.chipseq_bam2BG_out != "") {
+ publishDir "results/${params.chipseq_bam2BG_out}", mode: 'copy'
+ }
+
+ input:
+ tuple val(file_id), path(bam), path(idx)
+
+ output:
+ tuple val(file_id), path("*.bw"), emit: bw
+
+ script:
+"""
+bamCoverage -p ${task.cpus} -b ${bam} \
+ --binSize 10 \
+ --ignoreDuplicates \
+ --extendReads 200 \
+ --effectiveGenomeSize 2913022398 \
+ -o ${bam.simpleName}.bw \
+"""
+}
\ No newline at end of file
--
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