Added CLI command for generating a QC report for CDM

[mhkc]

Added a CLI command for generating the a QC report for CDM in JSON format. The PR includes a unit tests for the command.

Run

Run with prp create-cdm-input -q quast.tsv -p bwa.qc -c chewbbaca.out sample_name

Test

pytest tests

[ryanjameskennedy]

I was thinking that we could run prp just once like so:

prp create-output \\
      --sample-id ${sampleName} \\
      ${amrfinderArgs} \\
      ${brackenArgs} \\
      ${cgmlstArgs} \\
      ${mlstArgs} \\
      ${mykrobeArgs} \\
      ${postalignqcArgs} \\
      ${quastArgs} \\
      ${resfinderArgs} \\
      ${runInfoArgs} \\
      ${tbprofilerArgs} \\
      ${virulenceArgs} \\
      --qc-results ${qcOutput} \\
      --analysis-results ${output}

This way we don't need to parse the outputs twice?

[mhkc]

I think its cleaner to keep them as separate commands as it makes it clearer what type of input is used to generate which output. CDM is also a proprietary software that other sites are not going to use. Its cleaner to not generate CDM input data by default, especially since we already have a export_to_cdm submodule.

[ryanjameskennedy]

Yeah but the export_to_cdm is just for creating the arguments file for the upload:

echo ${sequencingRun} \\
         -sample-id ${sampleName} \\
         -assay ${species} \\
         -qc ${qc} \\
         ${limsID}

Anyways I will create another process in the prp module if you think this is better.

[ryanjameskennedy]

Perhaps we could add an --output arg?

[ryanjameskennedy]

Does this mean the subarg changes from create-output to create-bonsai-input? I.e. prp create-bonsai-input $args?

[ryanjameskennedy]

LGTM!