From 7b259f185cf57a22bab6abc2a7b5040c6d58ed8f Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Thu, 4 Feb 2021 09:21:31 +0100
Subject: [PATCH] [TEST] update test parameters
---
conf/test.config | 8 ++++----
main.nf | 19 ++++++++++---------
2 files changed, 14 insertions(+), 13 deletions(-)
diff --git a/conf/test.config b/conf/test.config
index 08dfcfc..a08cfe8 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -30,8 +30,8 @@ params {
min_insert_size = 100
max_insert_size = 600
- bin_size = '10000'
- //skip_mcool = true
- //skip_tads = true
- skip_dist_decay = true
+ bin_size = '1000'
+ res_dist_decay = '1000'
+ res_tads = '1000'
+ tads_caller = 'insulation,hicexplorer'
}
diff --git a/main.nf b/main.nf
index 3f7c09d..f1c597a 100644
--- a/main.nf
+++ b/main.nf
@@ -916,7 +916,7 @@ process cooler_balance {
file chrsize from chrsize_balance.collect()
output:
- set val(sample), val(res), file("${sample}_${res}_norm.cool") into norm_cool_maps, norm_cool_maps_h5
+ set val(sample), val(res), file("${sample}_${res}_norm.cool") into balanced_cool_maps
file("${sample}_${res}_norm.txt") into norm_txt_maps
script:
@@ -953,7 +953,6 @@ process cooler_zoomify {
/*
* Create h5 file
- */
process convert_to_h5 {
tag "$sample"
@@ -975,18 +974,20 @@ process convert_to_h5 {
--outputFormat h5 \
"""
}
-
+*/
/****************************************************
* DOWNSTREAM ANALYSIS
*/
+(maps_cool_insulation, maps_cool_comp, maps_hicexplorer_ddecay, maps_hicexplorer_tads) = balanced_cool_maps.into(4)
+
/*
* Counts vs distance QC
*/
if (!params.skip_dist_decay){
- chddecay = h5maps_ddecay.combine(ddecay_res).filter{ it[1] == it[3] }.dump(tag: "ddecay")
+ chddecay = maps_hicexplorer_ddecay.combine(ddecay_res).filter{ it[1] == it[3] }.dump(tag: "ddecay")
}else{
chddecay = Channel.empty()
}
@@ -1021,7 +1022,7 @@ process dist_decay {
/*
if(!params.skip_compartments){
- chcomp = iced_maps_comp.combine(comp_res).filter{ it[1] == it[4] }.dump(tag: "comp")
+ chcomp = maps_cool_comp.combine(comp_res).filter{ it[1] == it[4] }.dump(tag: "comp")
}else{
chcomp = Channel.empty()
}
@@ -1053,7 +1054,7 @@ process compartment_calling {
*/
if (!params.skip_tads){
- chtads = h5maps_tads.combine(tads_res_hicexplorer).filter{ it[1] == it[3] }.dump(tag: "hicexp")
+ chtads = maps_hicexplorer_tads.combine(tads_res_hicexplorer).filter{ it[1] == it[3] }.dump(tag: "hicexp")
}else{
chtads = Channel.empty()
}
@@ -1061,7 +1062,7 @@ if (!params.skip_tads){
process tads_hicexplorer {
tag "$sample - $res"
label 'process_medium'
- publishDir "${params.outdir}/tads", mode: 'copy'
+ publishDir "${params.outdir}/tads/hicexplorer", mode: 'copy'
when:
!params.skip_tads && params.tads_caller =~ 'hicexplorer'
@@ -1082,7 +1083,7 @@ process tads_hicexplorer {
}
if (!params.skip_tads){
- chIS = norm_cool_maps.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins")
+ chIS = maps_cool_insulation.combine(tads_res_insulation).filter{ it[1] == it[3] }.dump(tag : "ins")
}else{
chIS = Channel.empty()
}
@@ -1090,7 +1091,7 @@ if (!params.skip_tads){
process tads_insulation {
tag "$sample - $res"
label 'process_medium'
- publishDir "${params.outdir}/tads", mode: 'copy'
+ publishDir "${params.outdir}/tads/insulation", mode: 'copy'
when:
!params.skip_tads && params.tads_caller =~ 'insulation'
--
GitLab