From ed5b729c8dba9e938bf6dea4ccde75dca1eaa4ab Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Thu, 26 Oct 2023 17:21:36 +0200
Subject: [PATCH] bypass validation error for bin_size and co
---
lib/WorkflowHic.groovy | 17 +++++++++++++++++
nextflow.config | 2 +-
workflows/hic.nf | 22 ++++++++++++++++++----
3 files changed, 36 insertions(+), 5 deletions(-)
diff --git a/lib/WorkflowHic.groovy b/lib/WorkflowHic.groovy
index f14c26c..7e833dc 100755
--- a/lib/WorkflowHic.groovy
+++ b/lib/WorkflowHic.groovy
@@ -18,6 +18,11 @@ class WorkflowHic {
Nextflow.error "Unknown digestion protocol. Currently, the available digestion options are ${params.digest.keySet().join(", ")}. Please set manually the '--restriction_site' and '--ligation_site' parameters."
}
+ checkParamIntList(params.bin_size, log)
+ checkParamIntList(params.res_dist_decay, log)
+ checkParamIntList(params.res_tads, log)
+ checkParamIntList(params.res_compartments, log)
+
// Check Digestion or DNase Hi-C mode
//if (!params.dnase && !params.ligation_site) {
// Nextflow.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"
@@ -82,4 +87,16 @@ class WorkflowHic {
Nextflow.error(error_string)
}
}
+
+ // Check the params 'list of Integer' or Integer (ex bin_size)
+ public static void checkParamIntList(def param2check, log) {
+ if (param2check instanceof Integer || (param2check instanceof String && param2check ==~ /(\d+)(,\d+)*/)){
+ //good format, do nothing
+ }
+ else {
+ println "\n"
+ log.error "ERROR: ${param2check} must be integer or list of integer"
+ Nextflow.error('Exiting!')
+ }
+ }
}
diff --git a/nextflow.config b/nextflow.config
index abcab99..6fbc00c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -114,7 +114,7 @@ params {
version = false
validate_params = true
show_hidden_params = false
- schema_ignore_params = 'genomes,digest'
+ schema_ignore_params = 'genomes,digest,bin_size,res_dist_decay,res_tads,res_compartments'
// Config options
custom_config_version = 'master'
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 11c3d81..c53fd60 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -41,14 +41,22 @@ if (params.digestion){
//****************************************
// Combine all maps resolution for downstream analysis
-ch_map_res = Channel.from( params.bin_size ).splitCsv().flatten().toInteger()
+if (params.bin_size instanceof Integer) {
+ ch_map_res = Channel.from( params.bin_size ).toInteger()
+}
+else {
+ ch_map_res = Channel.from( params.bin_size ).splitCsv().flatten().toInteger()
+}
if (params.res_zoomify){
ch_zoom_res = Channel.from( params.res_zoomify ).splitCsv().flatten().toInteger()
ch_map_res = ch_map_res.concat(ch_zoom_res)
}
-if (params.res_tads && !params.skip_tads){
+if (params.res_tads && !params.skip_tads && params.res_tads instanceof Integer){
+ ch_tads_res = Channel.from( "${params.res_tads}" ).toInteger()
+ ch_map_res = ch_map_res.concat(ch_tads_res)
+}else if (params.res_tads && !params.skip_tads){
ch_tads_res = Channel.from( "${params.res_tads}" ).splitCsv().flatten().toInteger()
ch_map_res = ch_map_res.concat(ch_tads_res)
}else{
@@ -58,7 +66,10 @@ if (params.res_tads && !params.skip_tads){
}
}
-if (params.res_dist_decay && !params.skip_dist_decay){
+if (params.res_dist_decay && !params.skip_dist_decay && params.res_dist_decay instanceof Integer){
+ ch_ddecay_res = Channel.from( "${params.res_dist_decay}" ).toInteger()
+ ch_map_res = ch_map_res.concat(ch_ddecay_res)
+}else if (params.res_dist_decay && !params.skip_dist_decay){
ch_ddecay_res = Channel.from( "${params.res_dist_decay}" ).splitCsv().flatten().toInteger()
ch_map_res = ch_map_res.concat(ch_ddecay_res)
}else{
@@ -68,7 +79,10 @@ if (params.res_dist_decay && !params.skip_dist_decay){
}
}
-if (params.res_compartments && !params.skip_compartments){
+if (params.res_compartments && !params.skip_compartments && params.res_compartments instanceof Integer){
+ ch_comp_res = Channel.from( "${params.res_compartments}" ).toInteger()
+ ch_map_res = ch_map_res.concat(ch_comp_res)
+}else if (params.res_compartments && !params.skip_compartments){
ch_comp_res = Channel.from( "${params.res_compartments}" ).splitCsv().flatten().toInteger()
ch_map_res = ch_map_res.concat(ch_comp_res)
}else{
--
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