WDL Input Overview

This workflow splits a multi-sample VCF file into individual single-sample VCF files. This is achieved by first extracting all the samples from the provided multi-sample VCF file. The extracted samples are then broken up into "chunks" based on the specified chunk size. A new sample list is generated per chunk. Finally, this new "chunked" sample list is used to extract the corresponding samples from the original multi-sample VCF file, creating new single-sample VCF files. These files (and corresponding index files, if requested) are then copied to the specified output location.

Inputs:

| Parameter Name | Description | Type | Required | Default | |----------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------|----------|-----------------------------------------------------------------------------| | multiSampleVcf | The GCP path to the multi-sample VCF. | File | Yes | N/A | | outputLocation | Where the single-sample VCFs (and indices, if requested) should be written to. Note, the user running the workflow must have write permissions to this location. | String | Yes | N/A | | createIndexFiles | Whether index files should be generated for each extracted single-sample VCF file. | Boolean | No | true | | chunkSize | The number of samples that should be in each chunk. | Int | No | 1000 | | cpu | The number of CPU cores to allocate. | Int | No | 1 | | memoryMb | Memory allocation in megabytes. | Int | No | 6000 | | bcftoolsDocker | Docker image containing bcftools. | String | No | us.gcr.io/broad-gotc-prod/imputation-bcf-vcf:1.0.7-1.10.2-0.1.16-1669908889 | | diskSizeGb | The size of the VM's disk in GB. | Int | No | Calculated based on input multiSampleVcf file size |