fix: Remove unused parameter custom_extra_files (#51)

### Fixed

- Updated parameters documentation.

### Removed

- Unused parameter `custom_extra_files`.

Author: beatrizsavinhas

CHANGELOG.md

@@ -53,3 +53,4 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt
 ### `Removed`
 
 - Removed CI checks `awstest` and `awsfulltest` [#18](https://github.com/Clinical-Genomics/oncorefiner/pull/18)
+- Removed unused parameter `custom_extra_files` [#51](https://github.com/Clinical-Genomics/oncorefiner/pull/51)

docs/parameters.md

@@ -19,9 +19,9 @@ Reference genome related files and options required for the workflow.
 
 | Parameter | Description | Type | Default | Required | Hidden |
 |-----------|-----------|-----------|-----------|-----------|-----------|
+| `genome` | Name of the genome reference. (accepted: `GRCh38`\|`GRCh37`) <details><summary>Help</summary><small>Use this parameter to specify the ID for the reference genome used. This is then used to annotate the SV and SNV files e.g. `--genome GRCh38`.</small></details>| `string` | GRCh38 |  |  |
 | `fasta` | Path to FASTA genome file. <details><summary>Help</summary><small>If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.</small></details>| `string` |  |  |  |
 | `fai` | Path to FASTA genome index file. <details><summary>Help</summary><small>If none provided, will be generated automatically from the FASTA reference</small></details>| `string` |  |  |  |
-| `genome` | Name of the genome reference. (accepted: `GRCh38`\|`GRCh37`) <details><summary>Help</summary><small>Use this parameter to specify the ID for the reference genome used. This is then used to annotate the SV and SNV files e.g. `--genome GRCh38`.</small></details>| `string` | GRCh38 |  |  |
 | `species` | Species of the reference genome. E.g. `--species homo_sapiens`. (accepted: `homo_sapiens`) | `string` | homo_sapiens |  |  |
 
 ## Annotation options
@@ -81,4 +81,3 @@ Less common options for the pipeline, typically set in a config file.
 |-----------|-----------|-----------|-----------|-----------|-----------|
 | `snv_vcf` |  | `string` |  |  |  |
 | `sv_vcf` |  | `string` |  |  |  |
-| `custom_extra_files` |  | `string` |  |  |  |

nextflow.config

@@ -22,7 +22,6 @@ params {
     vep_cache_version           = 112
     vep_plugin_files            = null
     vep_cache                   = null
-    custom_extra_files          = null
 
     // Vcfanno
     vcfanno_toml                = null

nextflow_schema.json

@@ -339,9 +339,6 @@
         },
         "sv_vcf": {
             "type": "string"
-        },
-        "custom_extra_files": {
-            "type": "string"
         }
     }
 }

workflows/oncorefiner.nf

@@ -138,8 +138,7 @@ workflow ONCOREFINER {
             // VEP
             RESEARCH_FILTERING.out.vcf
                     .map { meta, vcf ->
-                        def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : []
-                        tuple(meta, vcf, custom_extra_files)
+                        tuple(meta, vcf, [])
                     }
                     .set { ch_vep_snv }
 
@@ -202,8 +201,7 @@ workflow ONCOREFINER {
             // VEP
             RESEARCH_FILTERING_SV.out.vcf
                 .map { meta, vcf ->
-                            def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : []
-                            tuple(meta, vcf, custom_extra_files) }
+                            tuple(meta, vcf, []) }
                 .set { ch_vep_sv }