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merged 3 commits into from
Sep 9, 2025
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add --maxentscan #284

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aa50f49
add --maxentscan
nvnieuwk Sep 9, 2025
6eaca7d
bump to 1.11.1dev
nvnieuwk Sep 9, 2025
ce0c22a
pre-commit
nvnieuwk Sep 9, 2025
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67 changes: 32 additions & 35 deletions .nf-core.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,53 +2,50 @@ bump_version:
lint:
actions_ci: false
files_exist:
- CODE_OF_CONDUCT.md
- assets/nf-core-smallvariants_logo_light.png
- docs/images/nf-core-smallvariants_logo_light.png
- docs/images/nf-core-smallvariants_logo_dark.png
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
- .github/workflows/template_version_comment.yml
- docs/README.md
- .github/workflows/nf-test.yml
│
- .github/actions/get-shards/action.yml
│
- .github/actions/nf-test/action.yml
│
- tests/default.nf.test
- CODE_OF_CONDUCT.md
- assets/nf-core-smallvariants_logo_light.png
- docs/images/nf-core-smallvariants_logo_light.png
- docs/images/nf-core-smallvariants_logo_dark.png
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
- .github/workflows/template_version_comment.yml
- docs/README.md
- .github/workflows/nf-test.yml │
- .github/actions/get-shards/action.yml │
- .github/actions/nf-test/action.yml │
- tests/default.nf.test
files_unchanged:
- .github/CONTRIBUTING.md
- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/branch.yml
- .github/workflows/linting_comment.yml
- .github/workflows/linting.yml
- CODE_OF_CONDUCT.md
- .github/ISSUE_TEMPLATE/bug_report.yml
- .prettierignore
- LICENSE
- .github/CONTRIBUTING.md
- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/branch.yml
- .github/workflows/linting_comment.yml
- .github/workflows/linting.yml
- CODE_OF_CONDUCT.md
- .github/ISSUE_TEMPLATE/bug_report.yml
- .prettierignore
- LICENSE
multiqc_config:
- report_comment
- report_comment
nextflow_config:
- custom_config
- manifest.name
- manifest.homePage
- validation.help.afterText
- validation.summary.afterText
- custom_config
- manifest.name
- manifest.homePage
- validation.help.afterText
- validation.summary.afterText
subworkflow_changes: false
nf_core_version: 3.2.0
repository_type: pipeline
template:
author: nvnieuwk
description: A nextflow pipeline for calling and annotating small
description: A nextflow pipeline for calling and annotating small
smallvariants variants from short DNA reads for WES and WGS data
force: false
is_nfcore: false
name: smallvariants
org: nf-cmgg
outdir: .
skip_features:
- fastqc
- is_nfcore
version: 1.12.0dev
- fastqc
- is_nfcore
version: 1.11.1dev
6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,12 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.11.1dev

## Changes

1. Added the `--maxentscan` parameter to specify the path to the MaxEntScan directory. This is required when using the MaxEntScan VEP plugin.

## v1.11.0 - Generous Ghent - [Sept 1 2025]

## New features
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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -274,7 +274,7 @@ process {
(params.vep_spliceai) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split('/')[-1]},indel=${params.spliceai_indel.split('/')[-1]}" : '',
(params.vep_spliceregion) ? '--plugin SpliceRegion' : '',
(params.vep_mastermind) ? "--plugin Mastermind,${params.mastermind.split('/')[-1]}" : '',
(params.vep_maxentscan) ? "--plugin MaxEntScan" : '',
(params.vep_maxentscan) ? "--plugin MaxEntScan,${params.maxentscan.split('/')[-1]}" : '',
(params.vep_alphamissense) ? "--plugin AlphaMissense,file=${params.alphamissense.split('/')[-1]}" : '',
(params.vep_eog) ? "--custom ${params.eog.split('/')[-1]},EOG,vcf,overlap,0,AF" : '',
(params.vep_merged) ? '--merged' : '',
Expand Down
1 change: 1 addition & 0 deletions docs/parameters.md
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Expand Up @@ -139,6 +139,7 @@ Parameters to configure Ensembl VEP and VCFanno
| `alphamissense_tbi` | Path to the index of the TSV for AlphaMissense. | `string` | | | |
| `eog` | Path to the VCF containing EOG annotations. | `string` | | | |
| `eog_tbi` | Path to the index of the VCF containing EOG annotations. | `string` | | | |
| `maxentscan` | Path to the directory containing the MaxEntScan reference annotations. | `string` | | | |
| `vcfanno` | Run annotations with vcfanno. | `boolean` | | | |
| `vcfanno_config` | The path to the VCFanno config TOML. | `string` | | | |
| `vcfanno_lua` | The path to a Lua script to be used in VCFanno. | `string` | | | |
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3 changes: 3 additions & 0 deletions main.nf
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Expand Up @@ -41,6 +41,7 @@ params.alphamissense = getGenomeAttribute('alphamissense', params.genomes
params.alphamissense_tbi = getGenomeAttribute('alphamissense_tbi', params.genomes, params.genome)
params.vcfanno_resources = getGenomeAttribute('vcfanno_resources', params.genomes, params.genome)
params.vcfanno_config = getGenomeAttribute('vcfanno_config', params.genomes, params.genome)
params.maxentscan = getGenomeAttribute('maxentscan', params.genomes, params.genome)

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -152,6 +153,7 @@ workflow {
params.eog_tbi,
params.alphamissense,
params.alphamissense_tbi,
params.maxentscan,
params.vcfanno_resources,
params.vcfanno_config,
params.multiqc_config,
Expand Down Expand Up @@ -186,6 +188,7 @@ workflow {
params.vep_mastermind,
params.vep_eog,
params.vep_alphamissense,
params.vep_maxentscan,

// Value inputs
params.genome,
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -279,7 +279,7 @@ manifest {
description = """A nextflow pipeline for calling and annotating small variants from short DNA reads for WES and WGS data"""
mainScript = 'main.nf'
nextflowVersion = '!>=25.04.0'
version = '1.12.0dev'
version = '1.11.1dev'
doi = ''
}

Expand Down
7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -658,6 +658,13 @@
"pattern": "^\\S+\\.(csi|tbi)$",
"exists": true
},
"maxentscan": {
"type": "string",
"format": "directory-path",
"description": "Path to the directory containing the MaxEntScan reference annotations.",
"pattern": "^\\S+$",
"exists": true
},
"vcfanno": {
"type": "boolean",
"description": "Run annotations with vcfanno."
Expand Down
10 changes: 10 additions & 0 deletions workflows/smallvariants.nf
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Expand Up @@ -87,6 +87,7 @@ workflow SMALLVARIANTS {
eog_tbi // string: path to the index of the EOG file
alphamissense // string: path to the Alphamissense file
alphamissense_tbi // string: path to the index of the Alphamissense file
maxentscan // string: path to the MaxEntScan directory
vcfanno_resources // string: semicolon-separated paths/globs to the VCFanno resources
vcfanno_config // string: path to VCFanno config TOML
multiqc_config // string: path to the multiqc config file
Expand Down Expand Up @@ -121,6 +122,7 @@ workflow SMALLVARIANTS {
vep_mastermind // boolean: use the Mastermind VEP plugin
vep_eog // boolean: use the EOG VEP plugin
vep_alphamissense // boolean: use the AlphaMissense VEP plugin
vep_maxentscan // boolean: use the MaxEntScan VEP plugin

// Value inputs
genome // string: the genome used by the pipeline run
Expand Down Expand Up @@ -222,6 +224,14 @@ workflow SMALLVARIANTS {
else if (vep_alphamissense) {
error("Please specify '--vep_alphamissense true', '--alphamissense PATH/TO/ALPHAMISSENSE/FILE' and '--alphamissense_tbi PATH/TO/ALPHAMISSENSE/INDEX/FILE' to use the AlphaMissense VEP plugin.")
}

// Check if all maxentscan files are given
if (maxentscan && vep_maxentscan) {
ch_vep_extra_files.add(file(maxentscan, checkIfExists: true))
}
else if (vep_maxentscan) {
error("Please specify '--vep_maxentscan true' and '--maxentscan PATH/TO/MAXENTSCAN/DIRECTORY' to use the MaxEntScan VEP plugin.")
}
}

//
Expand Down
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