From 3331539b0ce7d416ef6bc176c1246d5089e77082 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 7 Nov 2023 17:43:19 +0100
Subject: [PATCH] cleaning + add option skip plot matrix
---
nextflow.config | 1 +
nextflow_schema.json | 4 ++++
workflows/hic.nf | 15 ++++++---------
3 files changed, 11 insertions(+), 9 deletions(-)
diff --git a/nextflow.config b/nextflow.config
index 6fbc00c..31269f1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -93,6 +93,7 @@ params {
skip_compartments = false
skip_tads = false
skip_multiqc = false
+ skip_plot_matrix = false
// MultiQC options
multiqc_config = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index e5aeb17..753bab6 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -339,6 +339,10 @@
"skip_multiqc": {
"type": "boolean",
"description": "Do not generate MultiQC report"
+ },
+ "skip_plot_matrix": {
+ "type": "boolean",
+ "description": "Do not generate matrices"
}
}
},
diff --git a/workflows/hic.nf b/workflows/hic.nf
index 68b4ef8..67ccd43 100644
--- a/workflows/hic.nf
+++ b/workflows/hic.nf
@@ -41,12 +41,7 @@ if (params.digestion){
//****************************************
// Combine all maps resolution for downstream analysis
-/* 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()
-} */
+
ch_map_res = WorkflowHic.checkIfInt(params.bin_size)
if (params.res_zoomify){
@@ -223,10 +218,12 @@ workflow HIC {
//
// MODULE: HICEXPLORER/HIC_PLOT_MATRIX
//
- HIC_PLOT_MATRIX(
- COOLER.out.cool
- )
+ if (!params.skip_plot_matrix){
+ HIC_PLOT_MATRIX(
+ COOLER.out.cool
+ )
ch_versions = ch_versions.mix(HIC_PLOT_MATRIX.out.versions)
+ }
//
// SUB-WORKFLOW: COMPARTMENT CALLING
--
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