Modify input parameters to integrate with IRIDA-Next UI

[sgsutcliffe]

One of the main uses of staramrnf will be to be integrated with IRIDA-Next and so I am reformatting the input formatting to be properly integrated with IRIDA-Next user-interface. Changes should not impact the function of the pipeline.

PR checklist

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
• [x] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• [x] If necessary, also make a PR on the nf-core/staramr branch on the nf-core/test-datasets repository.
• [x] Make sure your code lints (nf-core lint).
• [x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [x] Usage Documentation in docs/usage.md is updated.
• [x] Output Documentation in docs/output.md is updated.
• [x] CHANGELOG.md is updated.
• [x] README.md is updated (including new tool citations and authors/contributors).

[sgsutcliffe]

The first change I made was to change the input column contigs to fastq_1 for the assembled genome that is input for staramr. This will break some nf-tests that point to an input file from dev branch but this will allow the IRIDA-Next UI to autopopulate the genome with whatever genome was uploaded.

[sgsutcliffe]

Changing contigs to fastq_1 worked but wasn't the right solution. See IRIDA Next Nextflow Pipeline Documentation, rather than using a fastq_1 file type I should create one for contigs

[sgsutcliffe]

The CLI arguments added to match the Galaxy staramr UI

[sgsutcliffe]

In addition to changing the MLST default name from "None" to "Automatic" I modified the function convert to be more flexible and accept species metadata from Kraken2.

[sgsutcliffe]

Removing the genomes param, is a default from nf-core template, and needs some additional files modified to allow it to be removed. See the iridanextexample