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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Just one sample in delivery folder when running multiple samples #40

Open parlundin opened 9 years ago

parlundin commented 9 years ago

When running multiple samples only one sample will end up in delivery folder. Overwriting?

johandahlberg commented 9 years ago

It's not overwriting - but since the directory is called delivery for all of the samples - and Piper looks for the .delivery.done file (which will be created by the first successfully finished run. Subsequent runs will thing that it's already done this and exit gracefully.

I will fix this by making sure that delivery is prefixed with the sample name when the --run_separately flag is enabled.

parlundin commented 9 years ago

If several samples running the second sample finish with ExitCode1, all vcf files generated and get error rm: cannot removetmp/': No such file or directory`. Guess this is related and will be fixed when above is fixed.

johandahlberg commented 9 years ago

Well - it's not exactly the same thing, but it relates to the same type of issue. If you point temp to be the same for all jobs the first one will remove it, and then it's gone.