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hammerlab / biokepi

Bioinformatics Ketrew Pipelines
Apache License 2.0
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Add Bfx.validate_bam #462

Open tavinathanson opened 7 years ago

tavinathanson commented 7 years ago

We want to ensure that, for example, failed runs of bwa-mem don't produce incomplete BAMs that might end up being processed downstream.

I'm not clear if I ran into this or whether this is a real concern, but there's a chance that I did and it is?

cc @ihodes @julia326

ihodes commented 7 years ago

My guess is the cleanup node of bwa-mem was killed before it could rm the truncated BAM, but this tool would be nice to have anyway.

smondet commented 7 years ago

Another thing we can do, is make bwa-mem (or any tool) write to a tmp-file and do a rename at the end of the job.