From 9912cc94d1067160305ad97547156bb59ad404a8 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Thu, 29 Jun 2023 11:35:52 +0200
Subject: [PATCH] try picard hicpro + delete temp bam sorted files
---
conf/modules.config | 4 ----
nextflow.config | 2 +-
subworkflows/local/filter_pcr_dup.nf | 16 +++++++++++-----
subworkflows/local/hicpro.nf | 18 +++++++++++++++++-
subworkflows/local/hicpro_mapping.nf | 28 +++-------------------------
5 files changed, 32 insertions(+), 36 deletions(-)
diff --git a/conf/modules.config b/conf/modules.config
index 01715bf..0b13690 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -424,9 +424,5 @@ process {
ext.args = { [
"-n"
].join('').trim() }
- publishDir = [
- path: { "${params.outdir}/picard/bam" },
- mode: 'copy'
- ]
}
}
diff --git a/nextflow.config b/nextflow.config
index f4f369b..6582b79 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -10,7 +10,7 @@
params {
// Choice of the workflow ('hicpro' or 'hicstuff')
- workflow = 'hicstuff'
+ workflow = 'hicpro'
// Input options
input = null
diff --git a/subworkflows/local/filter_pcr_dup.nf b/subworkflows/local/filter_pcr_dup.nf
index 3530d6f..344c1c9 100644
--- a/subworkflows/local/filter_pcr_dup.nf
+++ b/subworkflows/local/filter_pcr_dup.nf
@@ -32,13 +32,19 @@ workflow FILTER_PCR_DUP {
)
SAMTOOLS_SORT_N.out.bam.set{ ch_bam }
- FILTER_PAIR(
- ch_bam.combine(ch_bam)
- .map {
- meta1, bam1, meta2, bam2 ->
- meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null
+ if (params.workflow == "hicstuff"){
+ FILTER_PAIR(
+ ch_bam.combine(ch_bam)
+ .map {
+ meta1, bam1, meta2, bam2 ->
+ meta1.id == meta2.id && meta1.chunk == meta2.chunk && meta1.mates == "R1" && meta2.mates == "R2" ? [ meta1, bam1, meta2, bam2 ] : null
})
FILTER_PAIR.out.bam.set{ new_ch_bam }
+ }
+ else{
+ ch_bam.set{ new_ch_bam }
+ }
+
emit:
bam = new_ch_bam
diff --git a/subworkflows/local/hicpro.nf b/subworkflows/local/hicpro.nf
index 17543d0..6d2e07d 100644
--- a/subworkflows/local/hicpro.nf
+++ b/subworkflows/local/hicpro.nf
@@ -12,6 +12,7 @@ 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){
@@ -44,7 +45,22 @@ workflow HICPRO {
ch_versions = ch_versions.mix(HICPRO_MAPPING.out.versions)
HICPRO_MAPPING.out.bam.set{ ch_bam }
- ch_bam.view()
+
+ //***************************************
+ // 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}
+ }
//***************************************
// DIGESTION PROTOCOLS
diff --git a/subworkflows/local/hicpro_mapping.nf b/subworkflows/local/hicpro_mapping.nf
index 3e36cf0..61a95a8 100644
--- a/subworkflows/local/hicpro_mapping.nf
+++ b/subworkflows/local/hicpro_mapping.nf
@@ -9,7 +9,6 @@ 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
def pairToSingle(row, mates) {
@@ -31,12 +30,12 @@ def singleToPair(row){
return [ meta, row[1] ]
}
-def singleToPairPCR(row){
+/* def singleToPairPCR(row){
def meta = row[0].clone()
meta.remove('mates')
meta.single_end = false
return [ meta, [row[1], row[3]] ]
-}
+} */
workflow HICPRO_MAPPING {
@@ -111,28 +110,7 @@ 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 (
--
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