Flag to remove intermediate files about gatb-minia-pipeline HOT 4 OPEN

You can always remove the *hd5 files if your contig assemblies have finished ;)

Ofcourse I'm assuming this since you have reached the mapping stage.

I also tend to remove the glue files.

from gatb-minia-pipeline.

Yes, I do as well. I suppose it's a suggestion as an enhancement to the pipeline. During large assemblies where you aren't watching when to remove the files you may saturate a filesystem and cause the run to fail.

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I had the same issue and created a modified version that has a --cleanup flag that removes *.h5 and glu files after each iteration.
If one of the developers wants to review the code, I can make a PR. Otherwise I can just share the script if somebody ever needs it.

from gatb-minia-pipeline.

The script would be appreciated on my end, obviously I can't speak for the devs but it does seem like the ability to clean those files after each iteration would be highly desirable when assembling very large datasets.

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