From c4a7c59207cd323f52cfceab0dc6f972c557ab7e Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Wed, 3 May 2023 10:29:12 +0200
Subject: [PATCH] Different matrix building
---
conf/hicstuff.config | 14 ++++++++--
conf/modules.config | 9 ++++++
modules/local/hicexplorer/hicPlotMatrix.nf | 24 ++++++++++++++++
modules/local/hicstuff/bam2pairs.nf | 10 ++++---
.../local/hicstuff/build_matrix_cool_alt.nf | 28 +++++++++++++++++++
subworkflows/local/hicstuff_sub.nf | 17 +++++++++--
workflows/hicstuff.nf | 3 +-
7 files changed, 95 insertions(+), 10 deletions(-)
create mode 100644 modules/local/hicexplorer/hicPlotMatrix.nf
create mode 100644 modules/local/hicstuff/build_matrix_cool_alt.nf
diff --git a/conf/hicstuff.config b/conf/hicstuff.config
index e670077..0c0010d 100644
--- a/conf/hicstuff.config
+++ b/conf/hicstuff.config
@@ -130,6 +130,7 @@ params {
hicstuff_valid_idx = 'valid_idx.pairs'
hicstuff_min_qual = 30
hicstuff_matrix = 'abs_fragments_contacts_weighted.txt'
+ hicstuff_bin = 10000
}
process {
@@ -165,9 +166,9 @@ process {
}
withName: 'BAM2PAIRS' {
+ ext.pairs = params.hicstuff_valid_pairs
+ ext.index = params.hicstuff_valid_idx
ext.args = { [
- " -o ${params.hicstuff_valid_pairs}",
- " -x ${params.hicstuff_valid_idx}",
" -q ${params.hicstuff_min_qual}",
" -c ${params.hicstuff_circular}"
].join('').trim() }
@@ -190,6 +191,15 @@ process {
mode: 'copy'
]
}
+ withName: 'BUILD_MATRIX_COOL_ALT' {
+ ext.outname = params.hicstuff_matrix
+ ext.bin = params.hicstuff_bin
+ ext.args = {"-c1 2 -p1 3 -p2 4 -c2 5"}
+ publishDir = [
+ path: { "${params.outdir}/hicstuff/matrix" },
+ mode: 'copy'
+ ]
+ }
//**********************************************
// PREPARE_GENOME
diff --git a/conf/modules.config b/conf/modules.config
index 096a860..dc39872 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -286,4 +286,13 @@ process {
ext.args = '--correctForMultipleTesting fdr'
ext.prefix = { "${cool.baseName}" }
}
+
+ withName: 'HIC_PLOT_MATRIX' {
+ publishDir = [
+ path: { "${params.outdir}/contact_maps/cool/" },
+ mode: 'copy'
+ ]
+ ext.args = '--log --perChromosome'
+ ext.prefix = { "${cool.baseName}" }
+ }
}
diff --git a/modules/local/hicexplorer/hicPlotMatrix.nf b/modules/local/hicexplorer/hicPlotMatrix.nf
new file mode 100644
index 0000000..8041aa1
--- /dev/null
+++ b/modules/local/hicexplorer/hicPlotMatrix.nf
@@ -0,0 +1,24 @@
+process HIC_PLOT_MATRIX {
+ tag "$meta.id"
+ label 'process_single'
+
+ conda "bioconda::hicexplorer=3.7.2"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/hicexplorer:3.7.2--pyhdfd78af_1' :
+ 'quay.io/biocontainers/hicexplorer:3.7.2--pyhdfd78af_1' }"
+
+
+ input:
+ tuple val(meta), path(cool)
+
+ output:
+ tuple val(meta), path("*.pdf"), emit: pdf
+
+ script:
+ def args = task.ext.args ?: ''
+ def prefix = task.ext.prefix ?: "${meta.id}"
+
+ """
+ hicPlotMatrix -m ${cool} -o ${prefix}_cool_log.pdf ${args}
+ """
+}
diff --git a/modules/local/hicstuff/bam2pairs.nf b/modules/local/hicstuff/bam2pairs.nf
index c8a5a14..4b2b26e 100644
--- a/modules/local/hicstuff/bam2pairs.nf
+++ b/modules/local/hicstuff/bam2pairs.nf
@@ -1,5 +1,5 @@
process BAM2PAIRS {
- tag "$meta1"
+ tag "$meta1.id"
label 'process_high'
conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
@@ -12,15 +12,17 @@ process BAM2PAIRS {
tuple val(meta), path(fasta)
output:
- tuple val(meta1), path("valid.pairs"), emit: valid_pairs
- tuple val(meta1), path("valid_idx.pairs"), emit: idx_pairs
+ tuple val(meta1), path("*_valid.pairs"), emit: valid_pairs
+ tuple val(meta1), path("*_valid_idx.pairs"), emit: idx_pairs
script:
def args = task.ext.args ?: ''
+ def pairs = task.ext.pairs ?: ''
+ def index = task.ext.index ?: ''
"""
- hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -i ${info_contigs} -e ${digestion} -f ${fasta} ${args}
+ hicstuff_bam2pairs.py -b1 ${bam1} -b2 ${bam2} -i ${info_contigs} -e ${digestion} -f ${fasta} -o ${meta1.id}_${pairs} -x ${meta1.id}_${index} ${args}
"""
}
diff --git a/modules/local/hicstuff/build_matrix_cool_alt.nf b/modules/local/hicstuff/build_matrix_cool_alt.nf
new file mode 100644
index 0000000..a52465d
--- /dev/null
+++ b/modules/local/hicstuff/build_matrix_cool_alt.nf
@@ -0,0 +1,28 @@
+process BUILD_MATRIX_COOL_ALT {
+ tag "$meta1.id"
+ label 'process_single'
+
+ conda "conda-forge::python=3.9 conda-forge::biopython=1.80 conda-forge::numpy=1.22.3 conda-forge::matplotlib=3.6.3 conda-forge::pandas=1.5.3"
+ container = "lbmc/hicstuff:3.1.3"
+
+ input:
+ tuple val(meta), path(chromosome_size)
+ tuple val(meta1), path(idx_pairs)
+
+
+ output:
+ tuple val(meta), path("${meta1.id}_*.cool"), emit: matrix
+
+ script:
+
+ def args = task.ext.args ?: ''
+ def bin = task.ext.bin.toInteger() ?: ''
+ def outname = task.ext.outname ?: ''
+ def base = outname.replaceFirst(/.txt/,"")
+
+ """
+ cooler cload pairs ${args} ${chromosome_size}:${bin} ${idx_pairs} ${base}.cool
+
+ mv ${base}.cool ${meta1.id}_${base}_${bin}_alt.cool
+ """
+}
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index 60f1f79..47a005c 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -4,6 +4,7 @@ include { FRAGMENT_ENZYME } from '../../modules/local/hicstuff/fragment_enzyme'
include { BAM2PAIRS } from '../../modules/local/hicstuff/bam2pairs'
include { BUILD_MATRIX } from '../../modules/local/hicstuff/build_matrix'
include { BUILD_MATRIX_COOL } from '../../modules/local/hicstuff/build_matrix_cool'
+include { BUILD_MATRIX_COOL_ALT } from '../../modules/local/hicstuff/build_matrix_cool_alt'
// Paired-end to Single-end
def pairToSingle(row, mates) {
@@ -33,6 +34,7 @@ workflow HICSTUFF_SUB {
ligation_site
digestion
fasta
+ chromosome_size
main:
@@ -55,20 +57,29 @@ workflow HICSTUFF_SUB {
BOWTIE2_ALIGNMENT.out.bam.combine(BOWTIE2_ALIGNMENT.out.bam)
.map {
meta1, bam1, meta2, bam2 ->
- meta1.id == meta2.id && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null
+ meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null
},
FRAGMENT_ENZYME.out.info_contigs.collect(),
digestion,
fasta.collect()
)
+
+ //TODO rajouter filtres + distance law + filtres PCR en options
+ // pour les PCR filter, soit le hicstuff soit PICARD
+
BUILD_MATRIX(
BAM2PAIRS.out.idx_pairs,
- FRAGMENT_ENZYME.out.fragments_list
+ FRAGMENT_ENZYME.out.fragments_list.collect()
)
BUILD_MATRIX_COOL(
BAM2PAIRS.out.idx_pairs,
- FRAGMENT_ENZYME.out.fragments_list
+ FRAGMENT_ENZYME.out.fragments_list.collect()
+ )
+
+ BUILD_MATRIX_COOL_ALT(
+ chromosome_size.collect(),
+ BAM2PAIRS.out.idx_pairs
)
}
diff --git a/workflows/hicstuff.nf b/workflows/hicstuff.nf
index 4a69b68..8263bd3 100644
--- a/workflows/hicstuff.nf
+++ b/workflows/hicstuff.nf
@@ -39,6 +39,7 @@ workflow HICSTUFF {
PREPARE_GENOME.out.index,
ch_ligation_site,
params.digestion, //str enzyme
- ch_fasta
+ ch_fasta,
+ PREPARE_GENOME.out.chromosome_size
)
}
--
GitLab