From 882872dff32a8336935d5b6865976f9d41433da0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 31 Oct 2023 15:06:58 +0100 Subject: [PATCH] update usage of vep_version --- CHANGELOG.md | 1 + conf/modules/annotate.config | 2 +- nextflow.config | 1 + nextflow_schema.json | 7 +++++++ 4 files changed, 10 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1e35913229..fb310e1db8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1278](https://github.com/nf-core/sarek/pull/1278) - Hide sentieon parameters similar to other variant callers - [#1280](https://github.com/nf-core/sarek/pull/1280) - Replacing link to `SentieonDNAscopeModel1.1.model` in Sentieon's S3 with link to same file in igenomes' S3 +- [#1303](https://github.com/nf-core/sarek/pull/1303) - Ressurect vep_version params and changed its scope to pipeline to enable usage for vep loftee plugin ### Fixed diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config index 169acf7ec1..7356645add 100644 --- a/conf/modules/annotate.config +++ b/conf/modules/annotate.config @@ -37,7 +37,7 @@ process { ext.args = { [ (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_loftee) ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '', + (params.vep_loftee) ? "--plugin LoF,loftee_path://usr/local/share/ensembl-vep-${params.vep_version}" : '', (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf', diff --git a/nextflow.config b/nextflow.config index 09792cd134..88dcec4b09 100644 --- a/nextflow.config +++ b/nextflow.config @@ -95,6 +95,7 @@ params { vep_out_format = "vcf" vep_spliceai = null // spliceai plugin disabled within VEP vep_spliceregion = null // spliceregion plugin disabled within VEP + vep_version = "110.0-0" // Should be updated when we update VEP, needs this to get full path to some plugins bcftools_annotations = null // No extra annotation file bcftools_annotations_index = null // No extra annotation file index bcftools_header_lines = null // No header lines to be added to the VCF file diff --git a/nextflow_schema.json b/nextflow_schema.json index 5a84d9756f..4d008245f9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -540,6 +540,13 @@ "description": "Add an extra custom argument to VEP.", "help_text": "Using this params you can add custom args to VEP." }, + "vep_version": { + "type": "string", + "default": "110.0-0", + "fa_icon": "fas fa-toolbox", + "description": "Should reflect the VEP version used in the container.", + "help_text": "Used by the loftee plugin that need the full path." + }, "use_annotation_cache_keys": { "type": "boolean", "fa_icon": "fas fa-toolbox",