From 0e05a07d2bb5cb801ec2a89923024e66131bef62 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 22 Jan 2021 22:12:01 +0100
Subject: [PATCH] [MODIF] update skip options
---
main.nf | 17 ++++++++++++++---
nextflow.config | 4 +++-
2 files changed, 17 insertions(+), 4 deletions(-)
diff --git a/main.nf b/main.nf
index 2e42bab..91c3cf7 100644
--- a/main.nf
+++ b/main.nf
@@ -68,8 +68,10 @@ def helpMessage() {
Workflow
--skip_maps [bool] Skip generation of contact maps. Useful for capture-C. Default: False
- --skip_ice [bool] Skip ICE normalization. Default: False
- --skip_cool [bool] Skip generation of cool files. Default: False
+ --skip_balancing [bool] Skip contact maps normalization. Default: False
+ --skip_mcool Skip mcool file generation. Default: False
+ --skip_dist_decay Skip distance decay quality control. Default: False
+ --skip_tads [bool] Skip TADs calling. Default: False
--skip_multiqc [bool] Skip MultiQC. Default: False
Other options:
@@ -879,6 +881,9 @@ process cooler_build {
tag "$sample"
label 'process_medium'
+ when:
+ !params.skip_maps
+
input:
set val(sample), file(vpairs) from ch_vpairs_cool
file chrsize from chrsize_build.collect()
@@ -926,6 +931,9 @@ process cooler_balance {
publishDir "${params.outdir}/contact_maps/", mode: 'copy',
saveAs: {filename -> filename.indexOf(".cool") > 0 ? "norm/cool/$filename" : "norm/txt/$filename"}
+ when:
+ !params.skip_balancing
+
input:
set val(sample), val(res), file(cool) from raw_cool_maps
file chrsize from chrsize_balance.collect()
@@ -947,6 +955,9 @@ process cooler_zoomify {
label 'process_medium'
publishDir "${params.outdir}/contact_maps/norm/mcool", mode: 'copy'
+ when:
+ !params.skip_mcool
+
input:
set val(sample), file(contacts), file(index) from cool_build_zoom
file chrsize from chrsize_zoom.collect()
@@ -956,7 +967,7 @@ process cooler_zoomify {
script:
"""
- cooler makebins ${chrsize} 5000 > bins.bed
+ cooler makebins ${chrsize} ${params.res_zoomify} > bins.bed
cooler cload pairix --nproc ${task.cpus} bins.bed contacts.sorted.txt.gz ${sample}.cool
cooler zoomify --nproc ${task.cpus} --balance ${sample}.cool
"""
diff --git a/nextflow.config b/nextflow.config
index 71acfa7..57b95c5 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -69,11 +69,13 @@ params {
res_dist_decay = '1000000'
tads_caller = "hicexplorer,insulation"
res_tads = '40000,20000'
+ res_zoomify = '5000'
// Workflow
skip_maps = false
skip_ice = false
- skip_cool = false
+ skip_balancing = false
+ skip_mcool = false
skip_dist_decay = false
skip_tads = false
skip_multiqc = false
--
GitLab