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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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.done file generated but its not done #38

Open parlundin opened 9 years ago

parlundin commented 9 years ago

In folder 01 .done file is generated for a bam file but the bam file itself does not exist.

johandahlberg commented 9 years ago

This is related to the piping of bwa + samtools. I will fix it.

mariogiov commented 9 years ago

Hey Johan,

Do you think you will have some time to work on this soon? We're talking about doing something based on whether the alignment is done, still running, or failed, and at the moment I'm not sure we have any way of determining that.

johandahlberg commented 9 years ago

Well - this only happens if bwa + samtools fail (which should be relatively rare). So I think you should be safe creating functionallity that depends on this working as expected even if it might fail for a few edge-cases at the moment.

And of course I'll get around to this as fast as I can.

mariogiov commented 9 years ago

Ah, okay. Well I'll just proceed under the assumption that it works and we can deal with individual cases as they come up. Thanks!