fix: settings for ungrouped parameters

CHANGELOG.md

@@ -45,6 +45,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt
 - Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34)
 - Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45)
 - Added `species` parameter to provide information for annotation which was previously hardcoded [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49)
+- Added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50)
 
 ### `Dependencies`
 

docs/parameters.md

@@ -10,6 +10,8 @@ Define where the pipeline should find input data and save output data.
 |-----------|-----------|-----------|-----------|-----------|-----------|
 | `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>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.</small></details>| `string` |  | True |  |
 | `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` |  | True |  |
+| `snv_vcf` | Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses. | `string` |  |  |  |
+| `sv_vcf` | Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses. | `string` |  |  |  |
 | `email` | Email address for completion summary. <details><summary>Help</summary><small>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.</small></details>| `string` |  |  |  |
 | `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` |  |  |  |
 
@@ -74,10 +76,3 @@ Less common options for the pipeline, typically set in a config file.
 | `help` | Display the help message. | `['boolean', 'string']` |  |  |  |
 | `help_full` | Display the full detailed help message. | `boolean` |  |  |  |
 | `show_hidden` | Display hidden parameters in the help message (only works when --help or --help_full are provided). | `boolean` |  |  |  |
-
-## Other parameters
-
-| Parameter | Description | Type | Default | Required | Hidden |
-|-----------|-----------|-----------|-----------|-----------|-----------|
-| `snv_vcf` |  | `string` |  |  |  |
-| `sv_vcf` |  | `string` |  |  |  |

nextflow_schema.json

@@ -29,6 +29,22 @@
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
+                "snv_vcf": {
+                    "type": "string",
+                    "fa_icon": "fas fa-file",
+                    "description": "Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses.",
+                    "pattern": "^\\S+\\.vcf\\.gz$",
+                    "format": "file-path",
+                    "exists": true
+                },
+                "sv_vcf": {
+                    "type": "string",
+                    "fa_icon": "fas fa-file",
+                    "description": "Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses.",
+                    "pattern": "^\\S+\\.vcf\\.gz$",
+                    "format": "file-path",
+                    "exists": true
+                },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
@@ -333,12 +349,5 @@
             "$ref": "#/$defs/generic_options"
         }
     ],
-    "properties": {
-        "snv_vcf": {
-            "type": "string"
-        },
-        "sv_vcf": {
-            "type": "string"
-        }
-    }
+    "properties": {}
 }