From 6265b5a2ff61690bcdf7defcf11a7e15199666f0 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:04:44 +0100 Subject: [PATCH 1/3] Remove unused parameter custom_extra_files. --- docs/parameters.md | 3 +-- nextflow.config | 1 - nextflow_schema.json | 3 --- workflows/oncorefiner.nf | 6 ++---- 4 files changed, 3 insertions(+), 10 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index f6a5812..0457aba 100644 --- a/docs/parameters.md +++ b/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`)
HelpUse 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`.
| `string` | GRCh38 | | | | `fasta` | Path to FASTA genome file.
HelpIf 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.
| `string` | | | | | `fai` | Path to FASTA genome index file.
HelpIf none provided, will be generated automatically from the FASTA reference
| `string` | | | | -| `genome` | Name of the genome reference. (accepted: `GRCh38`\|`GRCh37`)
HelpUse 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`.
| `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` | | | | diff --git a/nextflow.config b/nextflow.config index a3778e5..37d5d46 100644 --- a/nextflow.config +++ b/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 diff --git a/nextflow_schema.json b/nextflow_schema.json index 0745a8e..4b2c414 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -339,9 +339,6 @@ }, "sv_vcf": { "type": "string" - }, - "custom_extra_files": { - "type": "string" } } } diff --git a/workflows/oncorefiner.nf b/workflows/oncorefiner.nf index 64ecec5..54a5f1b 100644 --- a/workflows/oncorefiner.nf +++ b/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 } From dd1b6eab6960921075574a58ceb8dc475f8377c8 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:07:04 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 76e536e..90f58fe 100644 --- a/CHANGELOG.md +++ b/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 `custom_extra_files` [#51](https://github.com/Clinical-Genomics/oncorefiner/pull/51) From 2293132b127cb172e5e89e71a1b61604425e1d54 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:09:59 +0100 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 90f58fe..c63aedb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -53,4 +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 `custom_extra_files` [#51](https://github.com/Clinical-Genomics/oncorefiner/pull/51) +- Removed unused parameter `custom_extra_files` [#51](https://github.com/Clinical-Genomics/oncorefiner/pull/51)