Do smrtsv2 have resume capability?

EichlerLab / smrtsv2

Structural variant caller

MIT License

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Do smrtsv2 have resume capability? #19

Closed rozaimirazali closed 5 years ago

rozaimirazali commented 5 years ago

Hi. Just wondering if smrtsv2 has resume capability?

For example, I am having a problem at a specific point in the Detect stage. If I re-run using the following command:

smrtsv align/alignments.fofn detect does it resume from the beginning of the Detect stage or the last point where I had encountered error previously?

paudano commented 5 years ago

It will pick up at the point where it left off in the detect stage. It will only re-run a rule if the rule did not complete, it's output is missing (and needed), or if there is a newer file upstream.