search

epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
Other
49 stars 36 forks source link

Option to output failed vcf #92

Closed ammaraziz closed 1 year ago

ammaraziz commented 1 year ago

Is your feature related to a problem?

When looking at positions in the consensus with Ns, it's useful to understand it has been masked/missing when genome coverage is high. The failed vcf contains very useful information.

Describe the solution you'd like

Similar to the .pass.named.vcf.gz output generated, please add a .fail.named.vcf.gz. The all_variants.vcf.gz output needs to contain the failed variants. Or ideally create two separate outputs all_failed_variants.vcf.gz and all_pass_variants.vcf.gz

Describe alternatives you've considered

Currently I search the work folder output by nextflow, however this is really difficult to search through as the outputs are in random folders.

Additional context

No response

mattdmem commented 1 year ago

Hi @ammaraziz,

Thanks for this suggestion. I agree that this will be a useful addition, if it doesn't make it to the current incarnation of wf-artic we will ensure masking reasons are enumerated in the replacement workflow.

Thanks

Matt