Clean up hifiasm module + add bin file input

[prototaxites]

• Tidy up hifiasm module code to have just a single script block, modifying inputs with variables
• Move -o option to directly before long_read input to ensure positional arguments are clearly separated from other arguments that can be lists of files
• Add optional input for .bin files to allow checkpointed resuming of a previous hifiasm run (e.g. to run in hi-c mode after running standard mode and reduce redundant computation)
• Reorganise output channels a bit
• Update nf-tests and add a test for resuming from bin files
• Add optional output channels for PAF and error-corrected FASTA, when requested

Questions:

• Is anyone using the separate .bin output channels? It might be cleaner to dump them out together but don't want to break anyone's workflow!

PR checklist

Closes #XXX

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[prototaxites]

I'm not sure what to do about the empty file linting tests - I don't think there's enough data in the tests to produce non-empty files

[SPPearce]

I'm not sure what to do about the empty file linting tests - I don't think there's enough data in the tests to produce non-empty files

Typically you then replace the md5sum test with a file existence check.

[prototaxites]

Typically you then replace the md5sum test with a file existence check.

Is this standard practice for e.g. stub tests? I don't think I've ever written a test that way before.

[SPPearce]

Typically you then replace the md5sum test with a file existence check.

Is this standard practice for e.g. stub tests? I don't think I've ever written a test that way before.

tests are allowed empty files provided they have "stub" in the name of the test

[fellen31]

Is anyone using the separate .bin output channels? It might be cleaner to dump them out together but don't want to break anyone's workflow!

Would there be any other use case for the bin files than to resume the run? Thanks for updating the module to make that possible!

[prototaxites]

Is anyone using the separate .bin output channels? It might be cleaner to dump them out together but don't want to break anyone's workflow!

Would there be any other use case for the bin files than to resume the run? Thanks for updating the module to make that possible!

I'm not aware of any other uses - you can dump some of the data out of them using hifiasm (e.g. --write-ec which will write the error-corrected reads bin file to fasta) - and am currently in the process of adding these outputs to the module. But I'm not aware that any other tool would use these outputs (and if you needed a specific one, you could still parse the output .bin file channel for the needed file).

[prototaxites]

OK, I've added optional outputs for the error-corrected reads, and read overlaps in PAF format. I've also collapsed the bin files to a single output channel. I've also updated the documentation to add a bit more useful description about the outputs.

If these changes look good to folk I can go ahead and merge.