subworkflows/vcf_extract_relate_somalier

The input VCFs to perform the stats on, optionally with their indices.
This channel can also contain the number of samples in the same family/group
to check relatedness. This is advised to add as it can improve the efficiency of your pipeline
Structure: [ val(meta), path(vcf), path(tbi), val(count) ]

The reference FASTA used to create the VCF files
Structure: [ path(fasta) ]

The index of the reference FASTA
Structure: [ path(fasta_fai) ]

A VCF containing the common sites for Somalier
Structure: [ path(somalier_sites_vcf) ]

A channel containing an optional PED file for the corresponding families. This channel has to be given, but can be like [meta, []].
When you don’t want to use a PED file, you must supply a channel
containing the meta and an empty value ([]) instead of a PED
Structure: [ val(meta), path(ped) ]

Optional - A text file describing how the samples should be grouped
Structure: [ path(txt) ]

Optional - A common identifier in the meta map.
This will be used to determine which VCFs should be used in somalier_relate.
This value should be given when using single sample VCFs