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ADD: new vep_custom_args #1041

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merged 7 commits into from
May 26, 2023
Merged

ADD: new vep_custom_args #1041

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20d9fff
ADD: vep_custom_args
maxulysse May 25, 2023
e37f67c
fix type
maxulysse May 25, 2023
87b17b6
use proper default value
maxulysse May 25, 2023
d964012
Update nextflow_schema.json
maxulysse May 25, 2023
ccd581b
Update nextflow_schema.json
maxulysse May 25, 2023
ffb4111
Update nextflow_schema.json
maxulysse May 25, 2023
ecbb3a0
Update nextflow_schema.json
maxulysse May 25, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#971](https://github.com/nf-core/sarek/pull/971) - Subtle bugfix to correct mutation of FASTP output channel objects
- [#978](https://github.com/nf-core/sarek/pull/978) - Validate that patient/sample does not contain spaces
- [#981](https://github.com/nf-core/sarek/pull/981) - Added documentation on generating ASCAT resources for exome and targeted sequencing
- [#1041](https://github.com/nf-core/sarek/pull/1041) - Add params `vep_custom_args` to let user specify custom params more easily for `VEP`

### Changed

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3 changes: 2 additions & 1 deletion conf/modules/annotate.config
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Expand Up @@ -42,7 +42,8 @@ process {
(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_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) ? "--${params.vep_out_format}" : '--vcf'
(params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf',
(params.vep_custom_args) ?: ''
].join(' ').trim() }
// If just VEP: <vcf prefix>_VEP.ann.vcf
ext.prefix = { "${vcf.baseName.minus(".vcf")}_VEP.ann" }
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -72,6 +72,7 @@ params {

// Annotation
vep_out_format = 'vcf'
vep_custom_args = null // No custom arguments for VEP
vep_dbnsfp = null // dbnsfp plugin disabled within VEP
dbnsfp = null // No dbnsfp processed file
dbnsfp_tbi = null // No dbnsfp processed file index
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7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -473,6 +473,13 @@
"hidden": true,
"help_text": "For details, see [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#spliceregion) and [here](https://www.ensembl.info/2018/10/26/cool-stuff-the-vep-can-do-splice-site-variant-annotation/)."
},
"vep_custom_args": {
"type": "string",
"fa_icon": "fas fa-toolbox",
"description": "Add an extra custom argument to VEP.",
"hidden": true,
"help_text": "Using this params you can add custom args to VEP."
},
"snpeff_cache": {
"type": "string",
"fa_icon": "fas fa-file",
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