feat(yallhap/classify): Add new module for Y-chromosome haplogroup classification#9704
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trianglegrrl wants to merge 1 commit intonf-core:masterfrom
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feat(yallhap/classify): Add new module for Y-chromosome haplogroup classification#9704trianglegrrl wants to merge 1 commit intonf-core:masterfrom
trianglegrrl wants to merge 1 commit intonf-core:masterfrom
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…assification Add yallhap/classify module for inferring Y-chromosome haplogroups from VCF files. Features: - Supports modern and ancient DNA samples - Uses YFull phylogenetic tree and YBrowse SNP database - Outputs JSON or TSV format with confidence scores - Compatible with GRCh37, GRCh38, and T2T references
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Hi @trianglegrrl, looks good - a couple of thoughts to start with.
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def format = task.ext.format ?: 'json' |
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Rather than adding a new task.ext directive, could you make this an input to the module (val format) instead?
| tag "yallhap" | ||
| tag "yallhap/classify" | ||
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| test("homo_sapiens - chrY vcf - stub") { |
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Is it possible to write a minimal test that is not a stub?
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Thanks for the snappy review! Just waiting for bioconda-recipes to accept my yallHap version bump before I push the updates here.
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(It comes with a test-datasets update and tests for classification of BAM and VCF formats. nf-core/test-datasets#1842)
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IMPORTANT: Requires this test-datasets PR:
nf-core/test-datasets#1842
Summary
Add new module
yallhap/classifyfor Y-chromosome haplogroup classification from VCF files.yallhap is a modern Y-chromosome haplogroup inference tool that supports:
Module inputs
Module outputs
PR checklist
nf-core modules lint yallhap/classifypasses (47 tests, 2 warnings about container links pending bioconda build propagation)Notes
The container link warnings are expected - yallhap 0.4.0 is available on bioconda but containers may still be building/propagating.
For ancient DNA samples with low coverage, users should pass
--min-depth 1 --min-quality 0viaext.args.