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

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

[apetkau]

This looks great Steven. Thanks so much 😄 . I have a few comments below.

I am also wondering if you could add some additional test cases where you adjust some of the parameters and then verify they were properly used in the staramr command. The output file settings.txt contains a copy of the full command-line string for staramr, so verifying that adjusted parameters for staramr could be done in test cases by reading this file and checking if the first line (the staramr command line) contains a string like e.g., --genome-size-lower-bound 4000000).

Example settings.txt:

command_line = staramr search --pointfinder-organism salmonella --genome-size-lower-bound 4000000 file.fasta

[apetkau]

This looks great. Thanks so much @sgsutcliffe 😄 . I have a few additional comments for you.

[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.

[apetkau]

Thanks so much for your changes Steven. I have a few more comments for you.

[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

[apetkau]

Thanks so much for all your amazing changes Steven :). One more in-line comment I have below.

[apetkau]

Everything looks great. Thanks so much Steven 😄

[kylacochrane]

This looks great Steven!