Create wave container for EXTRACT_METRICS local module

[JoseEspinosa]

Description of feature

Create wave container for EXTRACT_METRICS local module

[tlitfin]

May be cleaner to refactor extract_metrics to use different modules for each mode.

[JoseEspinosa]

May be cleaner to refactor extract_metrics to use different modules for each mode.

We can discuss it in the development meeting, but I think it could be easier to maintain a single common script than a module for each mode, although I agree it might be cleaner

[tlitfin]

I think the extract_metrics.py script in the bin/ directory can be common to all but we can decide whether or not to split the nextflow modules. One maintenance issue with having a single shared module is that we would need to test every mode whenever we make a change. Separate module keeps it more isolated and less likely to lead to unexpected bugs caused by conflicts between the modes.

The branching inside #554 already gets extremely complicated without all of the modes implemented. I think we should try to avoid this if possible. As separate modules they would should be a single line call to the python script.

[keiran-rowell-unsw]

I like Tom's suggestion of passing in, effectively, raw straight from RUN_PROGRAM to EXTRACT_METRICS. That way just a symlink gets passed without having to do any mv work or deal with the complicated branching in nf Tom mentions above, where there's lot of different file types and options. It hews close the exactly how the developer laid out their intermediate files.

extract_metrics.py can have --prog added to argparse and refactored to handle all sorts of program specific fun (#506, #490, #491, #576)

In #574 the program is now blissfully handled with meta.model as the routing switch

generate_report.py \\
    --report_type standard \\
    **--prog ${meta.model}** \\
    --msa ${msa} \\
    --pae ${pae} \\
    --structs ${pdb.join(' ')} \\
    --html_template ${template} \\
    --output_dir ./ \\
    --name ${meta.id} \\
    $args

extract_metrics.py could do similar