From 06e54f906b6928edc64be443488c65892498d0a9 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 24 Oct 2023 09:40:35 +0200
Subject: [PATCH] try skip param validation for bin_size
---
lib/WorkflowHic.groovy | 9 +++++++++
workflows/hic.nf | 24 +++++++++++++++++-------
2 files changed, 26 insertions(+), 7 deletions(-)
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
index 3dea732..0152384 100755
--- a/lib/WorkflowHic.groovy
+++ b/lib/WorkflowHic.groovy
@@ -18,6 +18,15 @@ class WorkflowHic {
System.exit(1)
}
+ if (params.bin_size instanceof Integer){
+ //skip
+ println("bin_size is int")
+ }
+
+ if (params.res_zoomify instanceof Integer){
+ //skip
+ println("res_zoomify is int")
+ }
// Check Digestion or DNase Hi-C mode
//if (!params.dnase && !params.ligation_site) {
// log.error "Ligation motif not found. Please either use the `--digestion` parameters or specify the `--restriction_site` and `--ligation_site`. For DNase Hi-C, please use '--dnase' option"
diff --git a/workflows/hic.nf b/workflows/hic.nf
index faa6a59..5c45e54 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -38,9 +38,19 @@ if (params.digestion){
//****************************************
// Combine all maps resolution for downstream analysis
-ch_map_res = Channel.from( params.bin_size ).splitCsv().flatten().toInteger()
+if (params.bin_size instanceof Integer) {
+ ch_map_res = Channel.from( params.bin_size ).toInteger()
+}
+else {
+ ch_map_res = Channel.from( params.bin_size ).splitCsv().flatten().toInteger()
+}
-if (params.res_zoomify){
+
+if (params.res_zoomify instanceof Integer){
+ ch_zoom_res = Channel.from( params.res_zoomify ).splitCsv().flatten().toInteger()
+ ch_map_res = ch_map_res.concat(ch_zoom_res)
+}
+else{
ch_zoom_res = Channel.from( params.res_zoomify ).splitCsv().flatten().toInteger()
ch_map_res = ch_map_res.concat(ch_zoom_res)
}
@@ -51,7 +61,7 @@ if (params.res_tads && !params.skip_tads){
}else{
ch_tads_res=Channel.empty()
if (!params.skip_tads){
- log.warn "[nf-core/hic] Hi-C resolution for TADs calling not specified. See --res_tads"
+ log.warn "[nf-core/hic] Hi-C resolution for TADs calling not specified. See --res_tads"
}
}
@@ -61,7 +71,7 @@ if (params.res_dist_decay && !params.skip_dist_decay){
}else{
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"
+ log.warn "[nf-core/hic] Hi-C resolution for distance decay not specified. See --res_dist_decay"
}
}
@@ -71,7 +81,7 @@ if (params.res_compartments && !params.skip_compartments){
}else{
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"
+ log.warn "[nf-core/hic] Hi-C resolution for compartment calling not specified. See --res_compartments"
}
}
@@ -96,7 +106,7 @@ ch_multiqc_custom_methods_description = params.multiqc_methods_description ? fil
//
// MODULE: Local to the pipeline
//
-include { HIC_PLOT_DIST_VS_COUNTS } from '../modules/local/hicexplorer/hicPlotDistVsCounts'
+include { HIC_PLOT_DIST_VS_COUNTS } from '../modules/local/hicexplorer/hicPlotDistVsCounts'
include { MULTIQC } from '../modules/local/multiqc'
//
@@ -236,7 +246,7 @@ workflow HIC {
.filter{ it[0].resolution == it[2] }
.map { it -> [it[0], it[1]]}
.set{ ch_cool_tads }
-
+
TADS(
ch_cool_tads
)
--
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