From 943242fb51dbc9699c6742f9a63f02a1c46fa7d2 Mon Sep 17 00:00:00 2001
From: Ksenia Krasheninnikova <kk16@sanger.ac.uk>
Date: Fri, 8 Sep 2023 11:52:17 +0100
Subject: [PATCH] Fixes for parameters descriptions

---
 nextflow_schema.json | 32 +++++++++++++++++---------------
 1 file changed, 17 insertions(+), 15 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index f6e92e57..33687f44 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -18,7 +18,7 @@
                     "mimetype": "text/yaml",
                     "pattern": "^\\S+\\.yaml$",
                     "schema": "assets/schema_input.json",
-                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
+                    "description": "Path to YAML file containing information about the dataset",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
                     "fa_icon": "fas fa-file-yaml"
                 },
@@ -35,33 +35,35 @@
                     "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                 },
-                "multiqc_title": {
-                    "type": "string",
-                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
-                    "fa_icon": "fas fa-file-signature"
-                },
                 "hifiasm_hic_on": {
-                    "type": "boolean"
+                    "type": "boolean",
+                    "description": "Switch on HiC mode for hifiasm assembly"
                 },
                 "polishing_on": {
-                    "type": "boolean"
+                    "type": "boolean",
+                    "description": "Switch on to do polish purged assembly before scaffolding"
                 },
                 "bed_chunks_polishing": {
                     "type": "integer",
-                    "default": 10
+                    "default": 10,
+                    "description": "Number of chunks to split fasta for polishing"
                 },
                 "cool_bin": {
                     "type": "integer",
-                    "default": 1000
+                    "default": 1000,
+                    "description": "Number of bins for cooler cload"
                 },
-                "hifiasmhic": {
-                    "type": "string"
+                "timestamp": {
+                    "type": "string",
+                    "hidden": true
                 },
                 "hifiasm": {
-                    "type": "string"
+                    "type": "string",
+                    "hidden": true
                 },
-                "timestamp": {
-                    "type": "string"
+                "hifiasmhic": {
+                    "type": "string",
+                    "hidden": true
                 }
             }
         },