From 8ab3d9c98adb6124c8d9735ac095fbb14720bde1 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Sun, 18 Jun 2023 07:44:39 +0000 Subject: [PATCH] add db param to schema --- nextflow_schema.json | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 05e5a83c4f..c2aed7463b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -238,6 +238,12 @@ "description": "If true, skips germline variant calling for matched normal to tumor sample. Normal samples without matched tumor will still be processed through germline variant calling tools.", "help_text": "This can speed up computation for somatic variant calling with matched normal samples. If false, all normal samples are processed as well through the germline variantcalling tools. If true, only somatic variant calling is done." }, + "genomicsdb_workspace": { + "type": "string", + "default": null, + "fa_icon": "fas fa-database", + "hidden": true + }, "joint_germline": { "type": "boolean", "fa_icon": "fas fa-toolbox", @@ -345,7 +351,7 @@ }, "cnvkit_reference": { "type": "string", - "default": null, + "default": "None", "fa_icon": "fas fa-file", "help_text": "https://cnvkit.readthedocs.io/en/stable/pipeline.html?highlight=reference.cnn#batch", "description": "Copy-number reference for CNVkit", @@ -528,7 +534,7 @@ "ascat_genome": { "type": "string", "fa_icon": "fa-solid fa-text", - "default": null, + "default": "None", "description": "ASCAT genome.", "help_text": "If you use AWS iGenomes, this has already been set for you appropriately.\n\nMust be set to run ASCAT, either hg19 or hg38. If you use AWS iGenomes, this has already been set for you appropriately.", "enum": ["None", "hg19", "hg38"],