Samplesheet multilevel nesting ick4

[jessicarowell]

This branch adds an option to choose which files to create the samplesheet (and thus, run the pipeline) on. It defaults to only running the pipeline on fastq files nested in subdirectories, the default CDC Core format. But you can instead choose to run the pipeline on all the files (top-nested and one-dir-under nested) or only the top-level files.

Test cmd:
nextflow run main.nf --indir /scicomp/groups-pure/Projects/scbs_mpob/JRowell_ick4/mpox_testing/paired/ --file_levels <nested, all, top> --outdir /scicomp/groups-pure/Projects/scbs_mpob/JRowell_ick4/mpox_testing/results/ --project_name test -config /scicomp/reference/nextflow/configs/cdc-dev.config -profile singularity,rosalind

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/mpxvassembly 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).

[mikeyweigand]

Please remove option --file_levels all because it utilizes inconsistent sample name derivation and reinforces poor data organization practices. Users should have option to define:
top -- look for fastq files in listed directory only
nested -- look for fastq files organized in subdirs one level down

in either scenario, ignore any other fastq files present in the directory tree passed to --indir.

[jessicarowell]

I have removed the --file_levels all option and updated the documentation to reflect this.

[mikeyweigand]

This needs some param validation because running with --file_levels all attempts to execute but returns warning:

NOTE: Process POLKAPOX_ASSEMBLY:POLKAPOX:CREATE_SAMPLESHEET terminated with an error exit status (2) -- Error is ignored

[jessicarowell]

I've enforced the valid values for --file_levels in nextflow

[mikeyweigand]

Looks good.