From 9fca40e574724c639b24f05963c9fc5d29665991 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Thu, 4 Feb 2021 13:05:43 +0100
Subject: [PATCH] [TEST] update test parameters
---
conf/test.config | 1 +
main.nf | 30 +++++++++++++++++++++---------
nextflow.config | 4 +++-
3 files changed, 25 insertions(+), 10 deletions(-)
diff --git a/conf/test.config b/conf/test.config
index a08cfe8..d06ad50 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -34,4 +34,5 @@ params {
res_dist_decay = '1000'
res_tads = '1000'
tads_caller = 'insulation,hicexplorer'
+ res_compartments = '1000'
}
diff --git a/main.nf b/main.nf
index f1c597a..382432f 100644
--- a/main.nf
+++ b/main.nf
@@ -277,9 +277,23 @@ if (params.res_dist_decay && !params.skip_dist_decay){
}
}
+if (params.res_compartments && !params.skip_compartments){
+ Channel.from( "${params.res_compartments}" )
+ .splitCsv()
+ .flatten()
+ .into {comp_bin; comp_res}
+ map_res = map_res.concat(comp_bin)
+ all_res = all_res + ',' + params.res_compartments
+}else{
+ comp_res = Channel.create()
+ if (!params.skip_compartments){
+ log.warn "[nf-core/hic] Hi-C resolution for compartment calling not specified. See --res_compartments"
+ }
+}
+
map_res
.unique()
- .into { map_res_summary; map_res; map_res_cool }
+ .into { map_res_summary; map_res; map_res_cool; map_comp }
/**********************************************************
* SET UP LOGS
@@ -1020,9 +1034,8 @@ process dist_decay {
* Compartment calling
*/
-/*
if(!params.skip_compartments){
- chcomp = maps_cool_comp.combine(comp_res).filter{ it[1] == it[4] }.dump(tag: "comp")
+ chcomp = maps_cool_comp.combine(comp_res).filter{ it[1] == it[3] }.dump(tag: "comp")
}else{
chcomp = Channel.empty()
}
@@ -1036,17 +1049,16 @@ process compartment_calling {
!params.skip_compartments
input:
- set val(sample), val(res), file(mat), file(bed), val(r) from chcomp
+ set val(sample), val(res), file(cool), val(r) from chcomp
output:
- file("*.bedgraph") optional true into out_compartments
+ file("*compartments*") optional true into out_compartments
script:
"""
- call_compartments.r --matrix ${mat} --bed ${bed}
+ cooltools call-compartments --contact-type cis -o ${sample}_compartments ${cool}
"""
}
-*/
/*
@@ -1068,14 +1080,14 @@ process tads_hicexplorer {
!params.skip_tads && params.tads_caller =~ 'hicexplorer'
input:
- set val(sample), val(res), file(h5mat), val(r) from chtads
+ set val(sample), val(res), file(cool), val(r) from chtads
output:
file("*.{bed,bedgraph,gff}") into hicexplorer_tads
script:
"""
- hicFindTADs --matrix ${h5mat} \
+ hicFindTADs --matrix ${cool} \
--outPrefix tad \
--correctForMultipleTesting fdr \
--numberOfProcessors ${task.cpus}
diff --git a/nextflow.config b/nextflow.config
index c3ddb38..6e8eae6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -60,6 +60,7 @@ params {
// Contact maps
bin_size = '1000000'
+ res_zoomify = '5000'
ice_max_iter = 100
ice_filer_low_count_perc = 0.02
ice_filer_high_count_perc = 0
@@ -69,7 +70,7 @@ params {
res_dist_decay = '250000'
tads_caller = 'insulation'
res_tads = '40000'
- res_zoomify = '5000'
+ res_compartments = '250000'
// Workflow
skip_maps = false
@@ -77,6 +78,7 @@ params {
skip_balancing = false
skip_mcool = false
skip_dist_decay = false
+ skip_compartments = false
skip_tads = false
skip_multiqc = false
--
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