Add nonpareil

[jfy133]

Add nonpareil metagenome redundancy estimation

Includes non-standard MultiQC output: the tool using R to generate a extrapolation plot.

The output from this is either a PNG or a R S3/S4 object that stores the raw data. There is no way to export the 'extrapolated' data as it is calculated in the plotting function. Therefore it's not really possible to add to MultiQC as otherwise it would require reconstructing the R function in python, and would involve computation in the MultiQC step.

Instead I've gone with adding a custom MultiQC section that embeds the PNG in the plot.

Example report here: multiqc.zip

PR checklist

• [x] This comment contains a description of changes (with reason).
• [ ] 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
• [ ] If necessary, also make a PR on the nf-core/taxprofiler 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).

[jfy133]

TODO: add nonpareil R based visualisation support ✅

[github-actions[bot]]

nf-core lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 40d1bfa

+| ✅ 159 tests passed       |+
!| ❗   2 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `main.nf`: _Remove this line if you don't need a FASTA file_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `methods_description_template.yml`: _#Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline_ ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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[jfy133]

@nf-core-bot fix linting

[Midnighter]

Is it the linting that touched so many files? It's a bit confusing, but Lili already approved so that's also fine 🙂 .

[jfy133]

Is it the linting that touched so many files? It's a bit confusing, but Lili already approved so that's also fine 🙂 .

This is nf-test for you... I added 3 modules and updated one.

Each comes with the typical ~3 module files, but for each module an additional 3-4 for nf-test and the conda env file, so doubling each. And then I updated quite a few test configs 🤷‍♀️

[jfy133]

Thanks @LilyAnderssonLee !