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Vep Issues: loftee needs version #706

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Aug 16, 2022
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Vep Issues: loftee needs version #706

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7497c28
fix loftee needing vep_version
FriederikeHanssen Aug 16, 2022
78e2054
Merge remote-tracking branch 'upstream/dev' into loftee
FriederikeHanssen Aug 16, 2022
eb4bc9c
update changelog
FriederikeHanssen Aug 16, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#688](https://github.com/nf-core/sarek/pull/688) - Fixed VEP plugins issue cf [#687](https://github.com/nf-core/sarek/issues/687)
- [#689](https://github.com/nf-core/sarek/pull/689) - Fixed when clause for non `BWA mem` building mapping indexes
- [#704](https://github.com/nf-core/sarek/pull/704) - Fixed `cf_ploidy` to string instead of number
- [#706](https://github.com/nf-core/sarek/pull/706) - Fixed `vep_version` not found error when running `--vep_loftee`

### Deprecated

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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -1208,15 +1208,15 @@ process{
// VEP
if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
withName: 'ENSEMBLVEP' {
ext.args = [
ext.args = { [
'--everything --filter_common --per_gene --total_length --offline --format vcf',
(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-${params.vep_version}-0" : '',
(params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${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'
].join(' ').trim()
].join(' ').trim() }
// If just VEP: <vcf prefix>_VEP.ann.vcf
ext.prefix = { "${vcf.baseName.minus(".vcf")}_VEP" }
if (!params.vep_cache) container = { params.vep_genome ? "nfcore/vep:${params.vep_version}.${params.vep_genome}" : "nfcore/vep:${params.vep_version}.${params.genome}" }
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