Just one sample in delivery folder when running multiple samples

[parlundin]

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

[johandahlberg]

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]

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

[johandahlberg]

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.