From a2843225a7d84c82749886c3a34cc650a3848c0e Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Mon, 19 Dec 2022 10:16:29 +0100
Subject: [PATCH] [MODULE] update cooltools
---
conf/modules.config | 4 ++--
modules/local/cooltools/eigscis.nf | 2 +-
modules/local/cooltools/insulation.nf | 4 ++--
subworkflows/local/tads.nf | 8 ++++----
4 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/conf/modules.config b/conf/modules.config
index 5b279c5..9eeb181 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -250,7 +250,7 @@ process {
//********************************
// COMPARTMENTS
- withName: 'CALL_COMPARTMENTS' {
+ withName: 'COOLTOOLS_EIGSCIS' {
publishDir = [
path: { "${params.outdir}/compartments/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
@@ -262,7 +262,7 @@ process {
//********************************
// TADS
- withName: 'INSULATION' {
+ withName: 'COOLTOOS_INSULATION' {
publishDir = [
path: { "${params.outdir}/tads/insulation/" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
diff --git a/modules/local/cooltools/eigscis.nf b/modules/local/cooltools/eigscis.nf
index 55d6d16..9af2a4d 100644
--- a/modules/local/cooltools/eigscis.nf
+++ b/modules/local/cooltools/eigscis.nf
@@ -2,7 +2,7 @@
* cooltools - call_compartments
*/
-process CALL_COMPARTMENTS {
+process COOLTOOLS_EIGSCIS {
label 'process_medium'
conda (params.enable_conda ? "bioconda::cooltools=0.5.1 bioconda::ucsc-bedgraphtobigwig=377" : null)
diff --git a/modules/local/cooltools/insulation.nf b/modules/local/cooltools/insulation.nf
index d6fd194..0d7f8be 100644
--- a/modules/local/cooltools/insulation.nf
+++ b/modules/local/cooltools/insulation.nf
@@ -2,7 +2,7 @@
* Cooltools - diamond-insulation
*/
-process INSULATION {
+process COOLER_INSULATION {
label 'process_medium'
conda (params.enable_conda ? "bioconda::cooltools=0.5.1" : null)
@@ -14,7 +14,7 @@ process INSULATION {
tuple val(meta), path(cool)
output:
- path("*tsv"), emit:results
+ path("*tsv"), emit:tsv
path("versions.yml"), emit:versions
script:
diff --git a/subworkflows/local/tads.nf b/subworkflows/local/tads.nf
index 5e7f4fc..31c1e38 100644
--- a/subworkflows/local/tads.nf
+++ b/subworkflows/local/tads.nf
@@ -1,4 +1,4 @@
-include { INSULATION } from '../../modules/local/cooltools/insulation'
+include { COOLTOOLS_INSULATION } from '../../modules/local/cooltools/insulation'
include { HIC_FIND_TADS } from '../../modules/local/hicexplorer/hicFindTADs'
workflow TADS {
@@ -11,9 +11,9 @@ workflow TADS {
ch_tads = Channel.empty()
if (params.tads_caller =~ 'insulation'){
- INSULATION(cool)
- ch_versions = ch_versions.mix(INSULATION.out.versions)
- ch_tads = ch_tads.mix(INSULATION.out.results)
+ COOLTOOLS_INSULATION(cool)
+ ch_versions = ch_versions.mix(COOLTOOLS_INSULATION.out.versions)
+ ch_tads = ch_tads.mix(COOLTOOLS_INSULATION.out.tsv)
}
if (params.tads_caller =~ 'hicexplorer'){
--
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