From 8ac65cc3b37336ec9e150564eee0338c4f25be01 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 19 Dec 2022 18:35:02 +0100
Subject: [PATCH] [MODIF] test --skip_compartment option #125
---
conf/modules.config | 4 ++--
nextflow.config | 4 ++--
workflows/hic.nf | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/conf/modules.config b/conf/modules.config
index 031e7c6..88d2ac5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -274,7 +274,7 @@ process {
mode: 'copy'
]
ext.args = '15 25 50 --window-pixels'
- ext.prefix = { "${meta.id}.${resolution}" }
+ ext.prefix = { "${cool.baseName}" }
}
withName: 'HIC_FIND_TADS' {
@@ -284,6 +284,6 @@ process {
mode: 'copy'
]
ext.args = '--correctForMultipleTesting fdr'
- ext.prefix = { "${meta.id}.${resolution}" }
+ ext.prefix = { "${cool.baseName}" }
}
}
diff --git a/nextflow.config b/nextflow.config
index 32176ea..cfddfeb 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -50,8 +50,8 @@ params {
ligation_site='GATCGATC'
}
'arima' {
- restriction_site='^GATC,G^ANT'
- ligation_site='GATCGATC,GANTGATC,GANTANTC,GATCANTC'
+ restriction_site='^GATC,G^ANTC'
+ ligation_site='GATCGATC,GATCANTC,GANTGATC,GANTANTC'
}
}
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 0f39687..362d51b 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -67,7 +67,7 @@ if (params.res_dist_decay && !params.skip_dist_decay){
.set {ch_ddecay_res}
ch_map_res = ch_map_res.concat(ch_ddecay_res)
}else{
- ch_ddecay_res = Channel.create()
+ ch_ddecay_res = Channel.empty()
if (!params.skip_dist_decay){
log.warn "[nf-core/hic] Hi-C resolution for distance decay not specified. See --res_dist_decay"
}
@@ -81,7 +81,7 @@ if (params.res_compartments && !params.skip_compartments){
.set {ch_comp_res}
ch_map_res = ch_map_res.concat(ch_comp_res)
}else{
- ch_comp_res = Channel.create()
+ ch_comp_res = Channel.empty()
if (!params.skip_compartments){
log.warn "[nf-core/hic] Hi-C resolution for compartment calling not specified. See --res_compartments"
}
--
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