das_tool: Use script not shell.

rhysnewell / aviary

A hybrid assembly and MAG recovery pipeline (and more!)

GNU General Public License v3.0

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das_tool: Use script not shell. #187

Closed wwood closed 7 months ago

wwood commented 7 months ago

Hey,

Basically converting the logic of the shell commands in the das_tool rule into a script, where a bit more care is taken.

There is a small functional difference. If a binning method has been run, but then rerun with that method in skip-binners. Previously bins from that binner were included, now they are not since the Fasta_to_Scaffolds2Bin script is only run for requested binners.

wwood commented 7 months ago

Does DAStool work if there is only 1 set of bins provided? I'm actually a bit confused why the test was working before I adjusted (it was only running semibin, I think)