vepyr: add an unnormalized multiallelic input VCF

[mwiewior]

Adds an unnormalized input VCF for the vcf_annotate_vepyr subworkflow (nf-core/modules#13070). The reviewer there noted that the existing input.vcf.gz has no multiallelic records, so the subworkflow's bcftools norm step changes nothing and is never really tested.

Files, data/genomics/homo_sapiens/vepyr/

File	Size	Content
input_multiallelic.vcf.gz + .tbi	39 KB	The same GIAB HG002 GRCh38 v4.2.1 window as input.vcf.gz (chr22:20572272-21735973), before normalization: 986 records, 14 of them multiallelic

It reuses the existing cache.tar.gz and reference.fa.gz, so nothing else is added.

Checked

• bcftools norm --fasta-ref reference.fa.gz -m -both --do-not-normalize (the subworkflow's documented configuration) splits 14 records into 28. The record body of the output is byte-identical to input.vcf.gz (md5 ca50096a40b2796376f02df03587516e). Normalizing this file and then annotating it should therefore give the same result as annotating input.vcf.gz.
• The files downloaded from this branch's raw URLs are byte-identical to the staged ones.
• The header is the benchmark VCF's own, with the local ##bcftools_*Command lines removed.

Generated by Claude Code

PR checklist

• I read the test-data specifications
• I tried testing my module with available data and there is no compatible data in test-datasets. No VCF here covers the vepyr cache window with multiallelic records.
• If I added data: I described the new files on the root README.md
• I made sure to submit the smallest dataset possible (e.g. try .tar.gz for larger directories)

[jonasscheid]

I think you dont need more testdata, you can use setup to manipulate right?

setup {
    run("UNTAR") { ... }   // unchanged
    run("BCFTOOLS_NORM", alias: "BCFTOOLS_JOIN_MULTIALLELICS") {
        script "modules/nf-core/bcftools/norm/main.nf"
        process {
            """
            input[0] = channel.of([
                [ id:'test_split' ],
                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/vepyr/input.vcf.gz', checkIfExists: true),
                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/vepyr/input.vcf.gz.tbi', checkIfExists: true)
            ])
            input[1] = channel.value([
                [ id:'GRCh38' ],
                file(params.modules_testdata_base_path + 'genomics/homo_sapiens/vepyr/reference.fa.gz', checkIfExists: true)
            ])
            """
        }
    }
}
// when: input[0] = BCFTOOLS_JOIN_MULTIALLELICS.out.vcf.map { _meta, vcf -> [ [ id:'test' ], vcf, [] ] }

It also needs this in tests/nextflow.config:

withName: 'BCFTOOLS_JOIN_MULTIALLELICS' {
    ext.args = '--multiallelics +both --output-type z'
}

Rest looks good to me

[mwiewior]

hey @jonasscheid thanks for the hint! I fixed that in the main sub-workflow PR. Closing this one.