vcf_phase_shapeit5

Subworkflow to phase a reference panel VCF file using SHAPEIT5. The panel is first chunked by chromosome by glimpse2/chunk, then genotypes are phased with shapeit5/phasecommon and finally the chunks are merged back together by shapeit5/ligate by chromosomes. Meta map of all channels will be used to perform joint operations. “regionout” key will be added to the meta map to distinguish the different file before ligation and therefore should not be used.

VCFphaseshapeit5haplotype

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/vcf_phase_shapeit5

Description

Input

name

description

pattern

`ch_vcf`

Channel with target VCF files

`ch_chunks`

Channel with region data

`ch_ref`

Channel with reference phased VCF files

`ch_scaffold`

Channel with reference scaffold VCF files

`ch_map`

Channel with genetic map data (optional)

`chunk`

Whether to perform chunking of the input data before imputation.

`chunk_model`

Chunk model for GLIMPSE2_chunk

Output

name

description

pattern

`chunks`

Channel with chunks regions

`vcf_index`

Channel with phased VCF files

`versions`

Channel containing software versions file