vcf_gather_bcftools

Concatenate several VCF files using bcftools concat. An additional option can be given to sort the concatenated VCF.

concatvcfgathersortbcftools

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

Description

Concatenate several VCF files using bcftools concat. An additional option can be given to sort the concatenated VCF.

Input

name

description

pattern

`ch_vcfs`

VCF files and their indices that should be concatenated, as well as the
expected number of VCFs per group. The meta map must contain at least a
common field for each VCF that needs to be merged,
e.g. [ id:‘test.001’, common_meta:‘test’ ]

Structure: [ val(meta), path(vcf), path(tbi), val(count) ]

`arr_common_meta`

OPTIONAL:
A string array of the common meta keys to use to group the vcfs.
Please make sure all VCFs that need to be concatenated have the same value in the
the meta fields specified - the subworkflow will error if a required key is missing from a meta map.

`val_sort`

Whether or not to sort the output VCF,
this can be useful if this subworkflow isn’t used in a scatter/gather workflow

Output

name

description

pattern

`vcf`

The concatenated (and possibly sorted) VCF file
Structure: [ val(meta), path(vcf) ]

*.vcf.gz

`index`

The indices of the output VCFs
Structure: [ val(meta), path(index) ]

*.vcf.gz.{tbi,csi}

`vcf_index`

Aggregated channel with the vcf and indices
Structure: [ val(meta), path(vcf), path(index) ]