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fix: VEP - Unknown method invocation on ArrayList type #587

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Merged
maxulysse merged 3 commits into from
Jun 13, 2022
Merged

fix: VEP - Unknown method invocation on ArrayList type #587

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bbabbb5
fix: Unknown method invocation on ArrayList type. It should have bee…
maxulysse Jun 13, 2022
e8c30bb
actually I think it should really have been an array all along
maxulysse Jun 13, 2022
8313f6e
update CHANGELOG
maxulysse Jun 13, 2022
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -84,7 +84,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#524](https://github.com/nf-core/sarek/pull/524) - Fix intervals usage by counting the actual list of scatter/gather files produced and not overall number of intervals
- [#549](https://github.com/nf-core/sarek/pull/549) - Fix unique lanes required for Freebayes: issue [#311](https://github.com/nf-core/sarek/issues/311), replaces `meta.clone()` with actual copy of map to avoid issues with <https://nfcore.slack.com/archives/C027CM7P08M/p1644241819942339>
- [#567](https://github.com/nf-core/sarek/pull/567) - Fix interval name resolving during scatter/gather by moving logic to modules.config causing name to be correctly resolved on process execution; also fixed duplicate naming when variant callers produce multiple vcf files by adding field `type` to `meta` map
- [#585](https://github.com/nf-core/sarek/pull/585) - Fix Spark usage for GATK4 modules.
- [#585](https://github.com/nf-core/sarek/pull/585) - Fix Spark usage for GATK4 modules
- [#587](https://github.com/nf-core/sarek/pull/587) - Fix issue with VEP extra files

### Deprecated

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16 changes: 6 additions & 10 deletions workflows/sarek.nf
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Expand Up @@ -103,19 +103,15 @@ vep_cache = params.vep_cache ? Channel.fromPath(params.vep_cac
vep_extra_files = []

if (params.dbnsfp && params.dbnsfp_tbi) {
vep_extra_files = vep_extra_files.mix(
Channel.fromPath(params.dbnsfp),
Channel.fromPath(params.dbnsfp_tbi)
).collect()
vep_extra_files.add(file(params.dbnsfp, checkIfExists: true))
vep_extra_files.add(file(params.dbnsfp_tbi, checkIfExists: true))
}

if (params.spliceai_snv && params.spliceai_snv_tbi && params.spliceai_indel && params.spliceai_indel_tbi) {
vep_extra_files = vep_extra_files.mix(
Channel.fromPath(params.spliceai_indel),
Channel.fromPath(params.spliceai_indel_tbi),
Channel.fromPath(params.spliceai_snv),
Channel.fromPath(params.spliceai_snv_tbi)
).collect()
vep_extra_files.add(file(params.spliceai_indel, checkIfExists: true))
vep_extra_files.add(file(params.spliceai_indel_tbi, checkIfExists: true))
vep_extra_files.add(file(params.spliceai_snv, checkIfExists: true))
vep_extra_files.add(file(params.spliceai_snv_tbi, checkIfExists: true))
}

// Initialize value channels based on params, not defined within the params.genomes[params.genome] scope
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