From 88d6463e64cc1c3d222a49ed01c40f9e7dcd7420 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Fri, 23 Jun 2023 09:36:24 +0200
Subject: [PATCH] TOFIX filter picard for hicpro correction
---
conf/modules.config | 16 ++++++------
subworkflows/local/hicpro.nf | 24 +++--------------
subworkflows/local/hicpro_mapping.nf | 39 +++++++++++++++++++++++++---
subworkflows/local/hicstuff_sub.nf | 5 ++++
workflows/hic.nf | 8 ++++++
5 files changed, 61 insertions(+), 31 deletions(-)
diff --git a/conf/modules.config b/conf/modules.config
index aea9de9..01715bf 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -389,14 +389,14 @@ process {
ext.prefix = { "${cool.baseName}" }
}
-// withName: 'HIC_PLOT_MATRIX' {
-// publishDir = [
-// path: { "${params.outdir}/contact_maps/cool/" },
-// mode: 'copy'
-// ]
-// ext.args = '--log --perChromosome'
-// ext.prefix = { "${cool.baseName}" }
-// }
+ withName: 'HIC_PLOT_MATRIX' {
+ publishDir = [
+ path: { "${params.outdir}/matrices/" },
+ mode: 'copy'
+ ]
+ ext.args = '--log --perChromosome'
+ ext.prefix = { "${cool.baseName}" }
+ }
//********************************
// FILTER_PCR_DUP
diff --git a/subworkflows/local/hicpro.nf b/subworkflows/local/hicpro.nf
index 0cea0ff..17543d0 100644
--- a/subworkflows/local/hicpro.nf
+++ b/subworkflows/local/hicpro.nf
@@ -12,7 +12,6 @@ include { MERGE_STATS } from '../../modules/local/hicpro/merge_stats'
include { HICPRO2PAIRS } from '../../modules/local/hicpro/hicpro2pairs'
include { BUILD_CONTACT_MAPS } from '../../modules/local/hicpro/build_contact_maps'
include { ICE_NORMALIZATION } from '../../modules/local/hicpro/run_ice'
-include { FILTER_PCR_DUP } from './filter_pcr_dup'
// Remove meta.chunks
def removeChunks(row){
@@ -39,28 +38,13 @@ workflow HICPRO {
HICPRO_MAPPING(
reads,
index,
- ligation_site
+ ligation_site,
+ fasta
)
ch_versions = ch_versions.mix(HICPRO_MAPPING.out.versions)
- //***************************************
- // FILTER PCR DUPLICATES
-
- if (params.filter_pcr_picard && !params.keep_dups){
- error "Error: cannot filter PCR duplicates with both methods! If filter_pcr_picard is true, keep_dups should be true too"
- }
- else if (params.filter_pcr_picard){
- FILTER_PCR_DUP(
- HICPRO_MAPPING.out.bam,
- fasta,
- index
- )
- FILTER_PCR_DUP.out.bam.set{ ch_bam }
- }
- else {
- HICPRO_MAPPING.out.bam.set{ ch_bam }
- }
-
+ HICPRO_MAPPING.out.bam.set{ ch_bam }
+ ch_bam.view()
//***************************************
// DIGESTION PROTOCOLS
diff --git a/subworkflows/local/hicpro_mapping.nf b/subworkflows/local/hicpro_mapping.nf
index 0f889e9..3e36cf0 100644
--- a/subworkflows/local/hicpro_mapping.nf
+++ b/subworkflows/local/hicpro_mapping.nf
@@ -9,8 +9,9 @@ include { BOWTIE2_ALIGN as BOWTIE2_ALIGN_TRIMMED } from '../../modules/nf-core/b
include { MERGE_BOWTIE2 } from '../../modules/local/hicpro/bowtie2_merge'
include { COMBINE_MATES} from '../../modules/local/hicpro/combine_mates'
include { MAPPING_STATS_DNASE } from '../../modules/local/hicpro/dnase_mapping_stats'
+include { FILTER_PCR_DUP } from './filter_pcr_dup'
-// Paired-end to Single-end
+// Paired-end to Single-end
def pairToSingle(row, mates) {
def meta = row[0].clone()
meta.single_end = true
@@ -30,6 +31,13 @@ def singleToPair(row){
return [ meta, row[1] ]
}
+def singleToPairPCR(row){
+ def meta = row[0].clone()
+ meta.remove('mates')
+ meta.single_end = false
+ return [ meta, [row[1], row[3]] ]
+}
+
workflow HICPRO_MAPPING {
@@ -37,10 +45,11 @@ workflow HICPRO_MAPPING {
reads // [meta, read1, read2]
index // [meta, path]
ligation_site // value
+ fasta
main:
ch_versions = Channel.empty()
-
+
// Align each mates separetly and add mates information in [meta]
ch_reads_r1 = reads.map{ it -> pairToSingle(it,"R1") }
ch_reads_r2 = reads.map{ it -> pairToSingle(it,"R2") }
@@ -82,7 +91,7 @@ workflow HICPRO_MAPPING {
)
ch_versions = ch_versions.mix(MERGE_BOWTIE2.out.versions)
ch_mapping_stats = MERGE_BOWTIE2.out.stats
-
+
// Combine mates
MERGE_BOWTIE2.out.bam
.map { singleToPair(it) }
@@ -102,6 +111,30 @@ workflow HICPRO_MAPPING {
.set {ch_bams}
}
+ //***************************************
+ // FILTER PCR DUPLICATES
+
+ if (params.filter_pcr_picard && !params.keep_dups){
+ error "Error: cannot filter PCR duplicates with both methods! If filter_pcr_picard is true, keep_dups should be true too"
+ }
+ else if (params.filter_pcr_picard){
+ if (!params.dnase){
+ MERGE_BOWTIE2.out.bam.set{ch_2filter}
+ }
+ else{
+ BOWTIE2_ALIGN.out.bamx.set{ch_2filter}
+ }
+ FILTER_PCR_DUP(
+ ch_2filter,
+ fasta,
+ index
+ )
+ FILTER_PCR_DUP.out.bam
+ .map { singleToPairPCR(it) }
+ .set {ch_bams}
+ }
+
+
COMBINE_MATES (
ch_bams
)
diff --git a/subworkflows/local/hicstuff_sub.nf b/subworkflows/local/hicstuff_sub.nf
index 28d383e..b3070d5 100644
--- a/subworkflows/local/hicstuff_sub.nf
+++ b/subworkflows/local/hicstuff_sub.nf
@@ -9,6 +9,7 @@ include { FILTER_EVENT } from '../../modules/local/hicstuff/filter_event'
include { DISTANCE_LAW } from '../../modules/local/hicstuff/distance_law'
include { FILTER_PCR } from '../../modules/local/hicstuff/filter_pcr'
include { FILTER_PCR_DUP } from './filter_pcr_dup'
+include { HIC_PLOT_MATRIX} from '../../modules/local/hicexplorer/hicPlotMatrix'
// Paired-end to Single-end
def pairToSingle(row, mates) {
@@ -126,4 +127,8 @@ workflow HICSTUFF_SUB {
chromosome_size.collect(),
ch_idx_pairs
)
+
+ HIC_PLOT_MATRIX(
+ BUILD_MATRIX_COOL_ALT.out.matrix
+ )
}
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 1b6b81e..830a4fa 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -100,6 +100,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
// MODULE: Local to the pipeline
//
include { HIC_PLOT_DIST_VS_COUNTS } from '../modules/local/hicexplorer/hicPlotDistVsCounts'
+include { HIC_PLOT_MATRIX } from '../modules/local/hicexplorer/hicPlotMatrix'
include { MULTIQC } from '../modules/local/multiqc'
//
@@ -213,6 +214,13 @@ workflow HIC {
ch_versions = ch_versions.mix(HIC_PLOT_DIST_VS_COUNTS.out.versions)
}
+ //
+ // MODULE: HICEXPLORER/HIC_PLOT_MATRIX
+ //
+ HIC_PLOT_MATRIX(
+ COOLER.out.cool
+ )
+
//
// SUB-WORKFLOW: COMPARTMENT CALLING
//
--
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