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epi2me-labs / wf-human-variation

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CNV subworkflow is not compatible with CRAM #25

Closed neurogenetics1 closed 1 year ago

neurogenetics1 commented 1 year ago

What happened?

A bug happened!

--cnv option yields an error with cram files that were generated by wf-basecalling. It requires a cram-bam conversion. Would it be possible to perform wf-human-variation --cnv option using only cram?

Operating System

ubuntu 18.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

wf-human-variation v1.3.0-gbc26fa0

Workflow Execution - CLI Execution Profile

Singularity

Workflow Version

wf-human-variation v1.3.0-gbc26fa0

Relevant log output

-
SamStudio8 commented 1 year ago

Hi @neurogenetics1, thanks for the report. Unfortunately the software inside the CNV subworkflow does not support CRAM. This is not ideal as wf-basecalling outputs CRAM by default! This is a known issue and we're working on a solution.

SamStudio8 commented 1 year ago

Thanks for your patience @neurogenetics1, as mentioned this is a limitation in the downstream software used in the CNV subworkflow. We have just released wf-human-variation 1.6.0 which addresses this in the short term by internally converting CRAM to BAM when calling for CNVs. Please let me know how you get on with this.