task SDtoBAF calls SiteDepthtoBAF without passing required index file

[simojoe]

Bug Report

Affected module(s) or script(s)

task SDtoBAF in wdl/BatchEvidenceMerging.wdl

Affected version(s)

• Latest public release version [0.28.4-beta]

Description

Task fails from a GATK User Error linked to missing index. (File paths were abridged).

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A USER ERROR has occurred: An index is required but was not found for file /cromwell-executions/[...]/Homo_sapiens_assembly38.dbsnp138.vcf.gz:/cromwell-executions/[...]/Homo_sapiens_assembly38.dbsnp138.vcf.gz. Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.

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This task calls GATK's SiteDepthtoBAF and one of its input, --baf-sites-vcf, requires a relevant index file.

Steps to reproduce

This workflow was ran with Cromwell on AWS Batch. This setup requires explicit input of index files size it cannot rely on having the index in the same location as the file.

Expected behavior

The task SDtoBAF should have an extra input field sd_locs_vcf_index to allow for the index to be passed (or it could be inferred in place by appending ".tbi"

This issue was solved on my setup by adding the index input file.