From e87e870b398f477c9f3a36448d0c26078d8e0f60 Mon Sep 17 00:00:00 2001
From: Mia Croiset <mia.croiset@ens-lyon.fr>
Date: Tue, 30 Jan 2024 13:30:19 +0100
Subject: [PATCH] update schema for cutsite
---
nextflow_schema.json | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index eda6d8b..f5f0617 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -714,6 +714,27 @@
"save_fragments": {
"type": "boolean",
"description": "Save fragments files"
+ },
+ "save_digested": {
+ "type": "boolean",
+ "description": "Save digested fastq files from cutsite process"
+ },
+ "cutsite": {
+ "type": "boolean",
+ "description": "If true, do cutsite process to pre digest reads"
+ },
+ "cutsite_cpu": {
+ "type": "integer",
+ "description": "Number of cpu to use for cutsite"
+ },
+ "cutsite_seed": {
+ "type": "integer",
+ "description": "Minimum size of a fragment (i.e. seed size used in mapping as reads smaller won't be mapped.)"
+ },
+ "cutsite_mode": {
+ "type": "string",
+ "description": "Mode to use to make the digestion.",
+ "enum": ["all", "for_vs_rev", "pile"]
}
}
}
--
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