I think this was bugged, it looks like bake doesn't move positional arguments to the end when the command is baked, and samtools expects the "-" to be at the end:
sh.samtools.view("-", b=True, S=True, u=True)
runs it like this:
samtools view - -b -S -u
which doesn't work. You can bake the keywords then bake the positional arguments after and that works though.
I think this was bugged, it looks like bake doesn't move positional arguments to the end when the command is baked, and samtools expects the "-" to be at the end:
runs it like this:
which doesn't work. You can bake the keywords then bake the positional arguments after and that works though.