Add new module: savana/run

[manascripts]

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[manascripts]

@SPPearce Thanks for the review on #11649!
I ran into history/branch divergence on the original PR while syncing with upstream, so I’ve opened a fresh one from a clean branch. I have incorporated your changes. The nesting outdir/${prefix} in the output is to avoid errors as savana run has a requirement: --outdir [OUTDIR] Output directory (can exist but must be empty)

[SPPearce]

Just don't force push, it should never be necessary.

[SPPearce]

So you can't set the output directory to be the current one? What if you give it the full path via pwd?
You could mv all the output files into the working directory after the tool has completed.

[manascripts]

Just don't force push, it should never be necessary.

Thanks, just to clarify: after git pull --rebase upstream master (suggested here), git push --force-with-lease becomes necessary, but I can merge upstream instead of rebasing going forward.

So you can't set the output directory to be the current one? What if you give it the full path via pwd? You could mv all the output files into the working directory after the tool has completed.

It complains about the dir not being empty, the requirement is an empty outdir, so using a fresh outdir inside the wd should work. Are you suggesting:
--outdir "$(pwd)/outdir" then mv outdir/* .? Do you think this would be better?

Also, the Singularity CI failure is a timeout while pulling the container image!