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Replace vcffixup for bcftools_filltags#300

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atrigila merged 14 commits into
nf-core:devfrom
atrigila:vcffixup
Jul 6, 2026
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Replace vcffixup for bcftools_filltags#300
atrigila merged 14 commits into
nf-core:devfrom
atrigila:vcffixup

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@atrigila

@atrigila atrigila commented Jun 21, 2026

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I replaced vcffixup for bcftools +fill-tags. bcftools +fill-tags reduced the frequency-computation process time from approximately 5 seconds to about 0.4 seconds per test chromosome (tested with Normalize vcf with computing frequencies after removing samples).

@atrigila atrigila marked this pull request as ready for review June 22, 2026 00:10
@atrigila atrigila requested a review from LouisLeNezet June 22, 2026 00:10

@LouisLeNezet LouisLeNezet left a comment

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Just a small change for the bibliography and a question about the change.

Comment thread subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf Outdated
Comment thread subworkflows/local/vcf_normalize_bcftools/tests/main.nf.test.snap
Comment thread subworkflows/local/utils_nfcore_phaseimpute_pipeline/tests/function.nf.test.snap Outdated
@atrigila atrigila requested a review from LouisLeNezet July 4, 2026 13:04

@LouisLeNezet LouisLeNezet left a comment

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LGTM

@atrigila atrigila merged commit 903ec44 into nf-core:dev Jul 6, 2026
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2 participants