From de475c48766565d52b81010aa6b71023d49345f8 Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Tue, 10 Oct 2023 19:57:59 +0000
Subject: [PATCH 1/3] consistency on hidden parameters

---
 nextflow_schema.json | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 68c6b77146..4dc2a8a1b1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -388,6 +388,7 @@
                     "type": "string",
                     "default": "variant",
                     "fa_icon": "fas fa-toolbox",
+                    "hidden": true,
                     "description": "Option for selecting output and emit-mode of Sentieon's Haplotyper.",
                     "help_text": "The option `--sentieon_haplotyper_emit_mode` can be set to the same string values as the Haplotyper's `--emit_mode`. To output both a vcf and a gvcf, specify both a vcf-option (currently, `all`, `confident` and `variant`) and `gvcf`. For example, to obtain a vcf and gvcf one could set `--sentieon_haplotyper_emit_mode` to `variant, gvcf`.",
                     "pattern": "^(all|confident|gvcf|variant|gvcf,all|gvcf,confident|gvcf,variant|all,gvcf|confident,gvcf|variant,gvcf)(?<!,)$"
@@ -396,6 +397,7 @@
                     "type": "string",
                     "default": "variant",
                     "fa_icon": "fas fa-toolbox",
+                    "hidden": true,
                     "description": "Option for selecting output and emit-mode of Sentieon's Dnascope.",
                     "help_text": "The option `--sentieon_dnascope_emit_mode` can be set to the same string values as the Dnascope's `--emit_mode`. To output both a vcf and a gvcf, specify both a vcf-option (currently, `all`, `confident` and `variant`) and `gvcf`. For example, to obtain a vcf and gvcf one could set `--sentieon_dnascope_emit_mode` to `variant, gvcf`.",
                     "pattern": "^(all|confident|gvcf|variant|gvcf,all|gvcf,confident|gvcf,variant|all,gvcf|confident,gvcf|variant,gvcf)(?<!,)$"
@@ -404,6 +406,7 @@
                     "type": "string",
                     "default": "CONSERVATIVE",
                     "fa_icon": "fas fa-bacon",
+                    "hidden": true,
                     "description": "Option for selecting the PCR indel model used by Sentieon Dnascope.",
                     "help_text": "PCR indel model used to weed out false positive indels more or less aggressively. The possible MODELs are: NONE (used for PCR free samples), and HOSTILE, AGGRESSIVE and CONSERVATIVE, in order of decreasing aggressiveness. The default value is CONSERVATIVE.",
                     "pattern": "^(NONE|HOSTILE|AGGRESSIVE|CONSERVATIVE)(?<!,)$"
@@ -411,6 +414,7 @@
                 "sentieon_dnascope_model": {
                     "type": "string",
                     "fa_icon": "fas fa-database",
+                    "hidden": true,
                     "description": "Machine learning model for Sentieon Dnascope.",
                     "help_text": " It is recommended to use DNAscope with a machine learning model to perform variant calling with higher accuracy by improving the candidate detection and filtering. Sentieon can provide you with a model trained using a subset of the data from the GiAB truth-set found in https://github.com/genome-in-a-bottle. In addition, Sentieon can assist you in the creation of models using your own data, which will calibrate the specifics of your sequencing and bio-informatics processing."
                 }

From 199d66d7a8549ffc3beb4d9c88a03da624c9ab47 Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Tue, 10 Oct 2023 20:00:34 +0000
Subject: [PATCH 2/3] update CHANGELOG [skip actions]

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 60d93f7426..37a11f87e0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [#1278](https://github.com/nf-core/sarek/pull/1278) - Hide sentieon parameters similar to other variant callers
+
 ### Fixed
 
 ### Dependencies

From 8bd5fdbfd762beb3732c3b01063536d1b93c2a61 Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Wed, 11 Oct 2023 08:38:36 +0000
Subject: [PATCH 3/3] trigger tests

---
 nextflow_schema.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4dc2a8a1b1..8a1a42095a 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -387,10 +387,10 @@
                 "sentieon_haplotyper_emit_mode": {
                     "type": "string",
                     "default": "variant",
-                    "fa_icon": "fas fa-toolbox",
-                    "hidden": true,
                     "description": "Option for selecting output and emit-mode of Sentieon's Haplotyper.",
+                    "fa_icon": "fas fa-toolbox",
                     "help_text": "The option `--sentieon_haplotyper_emit_mode` can be set to the same string values as the Haplotyper's `--emit_mode`. To output both a vcf and a gvcf, specify both a vcf-option (currently, `all`, `confident` and `variant`) and `gvcf`. For example, to obtain a vcf and gvcf one could set `--sentieon_haplotyper_emit_mode` to `variant, gvcf`.",
+                    "hidden": true,
                     "pattern": "^(all|confident|gvcf|variant|gvcf,all|gvcf,confident|gvcf,variant|all,gvcf|confident,gvcf|variant,gvcf)(?<!,)$"
                 },
                 "sentieon_dnascope_emit_mode": {