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Fix fasta index usage with genomes parameter #162

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Nov 25, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu) and [Mazza
- [#158](https://github.com/nf-core/phaseimpute/pull/158) - Fix contigs usage when regions is only a subset of the given contigs (e.g. if panel file has the 22 chr and the region file only 2 then only the 2 common will be processed). Fix `multiQC` samples names for better comprehension. Fix `-resume` errors when `ch_fasta` is use by adding `cache = 'lenient'` in necessary processes. Fix `--window-size` of `GLIMPSE_CHUNK` from `4` to `4000000`.
- [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
- [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
- [#162](https://github.com/nf-core/phaseimpute/pull/162) - Fix `fai` usage when provided by `genomes` parameter.

### `Dependencies`

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2 changes: 2 additions & 0 deletions subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,8 @@ workflow PIPELINE_INITIALISATION {
SAMTOOLS_FAIDX(ch_fasta, Channel.of([[], []]))
ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions.first())
fai = SAMTOOLS_FAIDX.out.fai.map{ it[1] }
} else {
fai = Channel.of(file(fai, checkIfExists:true))
}
} else if (params.fasta) {
genome = file(params.fasta, checkIfExists:true).getBaseName()
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