From 193e1e38d3b9de077ec160c115e7fe8311399bab Mon Sep 17 00:00:00 2001
From: Sam Nicholls <sam.nicholls@nanoporetech.com>
Date: Thu, 28 Nov 2024 17:04:18 +0000
Subject: [PATCH] Further simplify humvar in MinKNOW [CW-5355]

---
 CHANGELOG.md         |  1 +
 nextflow_schema.json | 18 ++++++++++++++----
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d131e1c..de0ec91 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Reconciled workflow with wf-template v5.3.1
 - Update Spectre to v0.3.2, which includes support for calling CNVs in hg19 data.
 - ClinVar version in SnpEff container updated to version 20241103.
+- Hidden additional options in MinKNOW for a simplified user experience.
 ### Added
 - `--spectre_args` may be used to provide custom arguments to the Spectre process.
 ### Fixed
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8fcbd4b..50f398c 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -243,7 +243,12 @@
                     "type": "boolean",
                     "default": false,
                     "description": "Perform phasing.",
-                    "help_text": "This option enables phasing of SV, SNP and modifications, depending on which sub-workflow has been chosen; see [README](README.md#9-phasing-variants) for more details."
+                    "help_text": "This option enables phasing of SV, SNP and modifications, depending on which sub-workflow has been chosen; see [README](README.md#9-phasing-variants) for more details.",
+                    "overrides": {
+                        "minknow": {
+                            "default": true
+                        }
+                    }
                 },
                 "include_all_ctgs": {
                     "type": "boolean",
@@ -252,7 +257,7 @@
                     "help_text": "Enabling this option will call for variants on all contigs of the input reference sequence. Typically this option is not required as standard human reference sequences contain decoy and unplaced contigs that are usually omitted for the purpose of variant calling. This option might be useful for non-standard reference sequence databases.",
                     "overrides": {
                         "minknow": {
-                            "title": "Include all contigs"
+                            "hidden": true
                         }
                     }
                 },
@@ -260,7 +265,12 @@
                     "type": "boolean",
                     "default": false,
                     "description": "If set to true, the workflow will generate gene-level coverage summaries.",
-                    "help_text": "If set to true, a 4-column BED file must be supplied, where column 4 is the gene label. The workflow will generate a list of all genes in the BED and their percentage coverage at a range of thresholds (1x, 10x, 15x, 20x, and 30x), as well as the average coverage of each gene."
+                    "help_text": "If set to true, a 4-column BED file must be supplied, where column 4 is the gene label. The workflow will generate a list of all genes in the BED and their percentage coverage at a range of thresholds (1x, 10x, 15x, 20x, and 30x), as well as the average coverage of each gene.",
+                    "overrides": {
+                        "minknow": {
+                            "hidden": true
+                        }
+                    }
                 },
                 "output_report": {
                     "type": "boolean",
@@ -548,7 +558,7 @@
                     ],
                     "overrides": {
                         "minknow": {
-                            "title": "Sex (XX or XY) to be passed to Straglr-genotype."
+                            "hidden": true
                         }
                     }
                 }