diff --git a/.nf-core.yml b/.nf-core.yml index 6129e6a5..2b2caa17 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,46 +2,43 @@ 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 @@ -49,6 +46,6 @@ template: org: nf-cmgg outdir: . skip_features: - - fastqc - - is_nfcore - version: 1.12.0dev + - fastqc + - is_nfcore + version: 1.11.1dev diff --git a/CHANGELOG.md b/CHANGELOG.md index 7f8c909b..869881d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/conf/modules.config b/conf/modules.config index 999afd35..74318a0b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -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' : '', diff --git a/docs/parameters.md b/docs/parameters.md index d69d3266..a23cfd54 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -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` | | | | diff --git a/main.nf b/main.nf index adef7055..43228ef1 100644 --- a/main.nf +++ b/main.nf @@ -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) /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -152,6 +153,7 @@ workflow { params.eog_tbi, params.alphamissense, params.alphamissense_tbi, + params.maxentscan, params.vcfanno_resources, params.vcfanno_config, params.multiqc_config, @@ -186,6 +188,7 @@ workflow { params.vep_mastermind, params.vep_eog, params.vep_alphamissense, + params.vep_maxentscan, // Value inputs params.genome, diff --git a/nextflow.config b/nextflow.config index 6122dbf7..f18d9fbf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 = '' } diff --git a/nextflow_schema.json b/nextflow_schema.json index 81b537d4..2449aed3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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." diff --git a/workflows/smallvariants.nf b/workflows/smallvariants.nf index 56a1ff30..c9488a13 100644 --- a/workflows/smallvariants.nf +++ b/workflows/smallvariants.nf @@ -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 @@ -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 @@ -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.") + } } //