From e533f0a5a5c87a28e8fb4eb065819062d981dcc0 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 22 Jan 2021 21:53:32 +0100
Subject: [PATCH] [MODIF] add zoomify
---
main.nf | 47 +++++++++++++++++++++++++++++------------------
1 file changed, 29 insertions(+), 18 deletions(-)
diff --git a/main.nf b/main.nf
index 6f660b6..a871e29 100644
--- a/main.nf
+++ b/main.nf
@@ -219,7 +219,7 @@ else {
// Chromosome size
if ( params.chromosome_size ){
Channel.fromPath( params.chromosome_size , checkIfExists: true)
- .into {chrsize; chrsize_build; chrsize_raw; chrsize_balance}
+ .into {chrsize; chrsize_build; chrsize_raw; chrsize_balance; chrsize_zoom}
}
else if ( params.fasta ){
Channel.fromPath( params.fasta )
@@ -438,7 +438,7 @@ if(!params.chromosome_size && params.fasta){
file fasta from fasta_for_chromsize
output:
- file "*.size" into chsize, chrsize_cool
+ file "*.size" into chrsize, chrsize_build, chrsize_raw, chrsize_balance, chrsize_zoom
script:
"""
@@ -681,7 +681,7 @@ if (!params.dnase){
process get_valid_interaction{
tag "$sample"
label 'process_low'
- publishDir "${params.outdir}/hic_results/data", mode: params.publish_dir_mode,
+ publishDir "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
input:
@@ -720,7 +720,7 @@ else{
process get_valid_interaction_dnase{
tag "$sample"
label 'process_low'
- publishDir "${params.outdir}/hic_results/data", mode: params.publish_dir_mode,
+ publishDir "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$filename" : "$filename"}
input:
@@ -753,7 +753,7 @@ else{
process remove_duplicates {
tag "$sample"
label 'process_highmem'
- publishDir "${params.outdir}/hic_results/data", mode: params.publish_dir_mode,
+ publishDir "${params.outdir}/valid_pairs", mode: params.publish_dir_mode,
saveAs: {filename -> filename.indexOf(".stat") > 0 ? "stats/$sample/$filename" : "$filename"}
input:
@@ -799,7 +799,7 @@ process remove_duplicates {
process merge_stats {
tag "$ext"
label 'process_low'
- publishDir "${params.outdir}/hic_results/stats/${sample}", mode: params.publish_dir_mode
+ publishDir "${params.outdir}/stats/${sample}", mode: params.publish_dir_mode
input:
set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
@@ -820,14 +820,14 @@ process merge_stats {
/*
* HiC-Pro build matrix processes
- * TODO - TO REPLACED BY COOLER ?
+ * ONGOING VALIDATION - TO REPLACED BY COOLER ?
*/
process build_contact_maps{
tag "$sample - $mres"
label 'process_highmem'
- publishDir "${params.outdir}/hic_results/matrix/raw", mode: params.publish_dir_mode
+ publishDir "${params.outdir}/hicpro/matrix/raw", mode: params.publish_dir_mode
when:
!params.skip_maps
@@ -848,7 +848,7 @@ process build_contact_maps{
process run_ice{
tag "$rmaps"
label 'process_highmem'
- publishDir "${params.outdir}/hic_results/matrix/iced", mode: params.publish_dir_mode
+ publishDir "${params.outdir}/hicpro/matrix/iced", mode: params.publish_dir_mode
when:
!params.skip_maps && !params.skip_ice
@@ -884,7 +884,7 @@ process cooler_build {
file chrsize from chrsize_build.collect()
output:
- set val(sample), file("contacts.sorted.txt.gz"), file("contacts.sorted.txt.gz.px2") into cool_build
+ set val(sample), file("contacts.sorted.txt.gz"), file("contacts.sorted.txt.gz.px2") into cool_build, cool_build_zoom
script:
"""
@@ -915,7 +915,7 @@ process cooler_raw {
"""
cooler makebins ${chrsize} ${res} > ${sample}_${res}.bed
cooler cload pairix --nproc ${task.cpus} ${sample}_${res}.bed ${contacts} ${sample}_${res}.cool
- cooler dump ${sample}_${res}.cool --one-based-ids | awk '{OFS="\t"; print \$1+1,\$2+1,\$3}' > ${sample}_${res}.txt
+ cooler dump ${sample}_${res}.cool | awk '{OFS="\t"; print \$1+1,\$2+1,\$3}' > ${sample}_${res}.txt
"""
}
@@ -938,18 +938,30 @@ process cooler_balance {
"""
cp ${cool} ${sample}_${res}_norm.cool
cooler balance ${sample}_${res}_norm.cool -p ${task.cpus} --force
- cooler dump ${sample}_${res}_norm.cool --one-based-ids --balanced --na-rep 0 | awk '{OFS="\t"; print \$1+1,\$2+1,\$4}' > ${sample}_${res}_norm.txt
+ cooler dump ${sample}_${res}_norm.cool --balanced --na-rep 0 | awk '{OFS="\t"; print \$1+1,\$2+1,\$4}' > ${sample}_${res}_norm.txt
"""
}
-/*
- -- TODO--
-
process cooler_zoomify {
+ tag "$sample"
+ label 'process_medium'
+ publishDir "${params.outdir}/contact_maps/norm/mcool", mode: 'copy'
+
+ input:
+ set val(sample), file(contacts), file(index) from cool_build_zoom
+ file chrsize from chrsize_zoom.collect()
+
+ output:
+ file("*mcool") into mcool_maps
+ script:
+ """
+ cooler makebins ${chrsize} 5000 > bins.bed
+ cooler cload pairix --nproc ${task.cpus} bins.bed contacts.sorted.txt.gz ${sample}.cool
+ cooler zoomify --nproc ${task.cpus} --balance ${sample}.cool
+ """
}
-*/
/*
* Create h5 file
@@ -990,7 +1002,7 @@ chddecay = h5maps_ddecay.combine(ddecay_res).filter{ it[1] == it[3] }.dump(tag:
process dist_decay {
tag "$sample"
label 'process_medium'
- publishDir "${params.outdir}/hic_results/dist", mode: 'copy'
+ publishDir "${params.outdir}/dist_decay", mode: 'copy'
when:
!params.skip_dist_decay
@@ -1065,7 +1077,6 @@ process tads_insulation {
}
-
/*
* MultiQC
*/
--
GitLab