Add first two modules (diamond and kaiju), missing docs and tests

[jfy133]

This is more of a PoC to draft rough structure. Subject to change during development.

~Note input validation not working correctly, as only need to require one of either fasta_dna or fasta_aa, or both. But if neither supplied then it just runs with empty lists :(~ now working thanks to @mirpedrol :D

Adds:

• Input schema sheet draft
• DIAMOND
• Kaiju

database building and nf-tests :)

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/createtaxdb 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).

[github-actions[bot]]

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

Posted for pipeline commit a317cbe

+| ✅ 160 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  21 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/readme.html) - README contains the placeholder `zenodo.XXXXXXX`. This should be replaced with the zenodo doi (after the first release). * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `nextflow.config`: _Specify your pipeline's command line flags_ * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_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/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _TODO nf-core:_ * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Include a figure that guides the user through the major workflow steps. Many nf-core_ * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Fill in short bullet-pointed list of the default steps in the pipeline_ * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets._ * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _update the following command to include all required parameters for a minimal example_ * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _If applicable, make list of people who have also contributed_ * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Add citation for pipeline after first release. 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Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - 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Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - nextflow.config contains configuration profile `test` * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - 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`.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.github/workflows/linting.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/nf-core-createtaxdb_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `docs/images/nf-core-createtaxdb_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `docs/images/nf-core-createtaxdb_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `lib/NfcoreTemplate.groovy` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.prettierignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `pyproject.toml` matches the template * [actions_awstest](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_awstest.html) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/readme.html) - README Nextflow minimum version badge matched config. Badge: `23.04.0`, Config: `23.04.0` * [pipeline_name_conventions](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/template_strings.html) - Did not find any Jinja template strings (104 files) * [schema_lint](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/csv' * [schema_params](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [system_exit](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/system_exit.html) - No `System.exit` calls found * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: release-announcments.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: awstest.yml * [merge_markers](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_section_order` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `export_plots` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_comment` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.11.1 * Run at `2024-01-05 16:36:02`

[jfy133]

I know this is very early work. I'm fine with merging as is but I had two concerns that I propose to change in the long run:

Do you mind if you give me an approval then I can merge this in and follow up depending on feedback of my status below? Then can start doing more parallel PRs to add the below

1. There are two separate input options for nodesdmp and namesdmp. I would expect a path/tar of a directory with those files (possibly containing more of the dump files).

Is expectation this based purely on ncbi taxdump files? I currently had kept it separate because if people want to make custom databases that may include customised dump files whereby I don't see why one would necessarily re-tar...

That said it is reasonable to expect someone may want to do that... I may consider adding it as an option (if one gives the taxdump as tar it'll auto extract - but I vaguely remember plucking specific files from a directory is not directly trivial with Nxf).

But I would make this a separate issue as a separate functionality (including maybe auto downloading taxdump files, but I'm not sure yet how to do this properly e.g. with gtdbtk taxdump stuff etc)

2. I would create one subworkflow per tool that the main createtaxdb workflow calls to.

Yes that's my plan for multi-module database construction commands (e.g. kraken2), or do you have a motivation to do this for single build modules too?

[Midnighter]

Do you mind if you give me an approval then I can merge this in and follow up depending on feedback of my status below?

I didn't approve due to the open comments. Do you plan to address them or see them as irrelevant?

Is expectation this based purely on ncbi taxdump files? I currently had kept it separate because if people want to make custom databases that may include customised dump files whereby I don't see why one would necessarily re-tar...

That said it is reasonable to expect someone may want to do that... I may consider adding it as an option (if one gives the taxdump as tar it'll auto extract - but I vaguely remember plucking specific files from a directory is not directly trivial with Nxf).

My expectation is based on taxonkit usage, yes. With a custom taxonomy I would just pass a path to a directory and then expect {dir}/nodes.dmp and {dir}/names.dmp to exist.

Yes that's my plan for multi-module database construction commands (e.g. kraken2), or do you have a motivation to do this for single build modules too?

No, I don't see a reason for single modules. I didn't read the file properly and somehow thought the input channel transformation was Kaiju-specific.

[jfy133]

Do you mind if you give me an approval then I can merge this in and follow up depending on feedback of my status below?

I didn't approve due to the open comments. Do you plan to address them or see them as irrelevant?

Hm, I thought I had addressed them 🤔, but I see now there is no commit. Maybe I didn't push...

Is expectation this based purely on ncbi taxdump files? I currently had kept it separate because if people want to make custom databases that may include customised dump files whereby I don't see why one would necessarily re-tar...

That said it is reasonable to expect someone may want to do that... I may consider adding it as an option (if one gives the taxdump as tar it'll auto extract - but I vaguely remember plucking specific files from a directory is not directly trivial with Nxf).

My expectation is based on taxonkit usage, yes. With a custom taxonomy I would just pass a path to a directory and then expect {dir}/nodes.dmp and {dir}/names.dmp to exist.

Hrm, ok. I'll maybe look more in detail to taxonkit and try and use that as a structure to follow. But I think I would still do that as a follow up PR (because it should be quite straightforward to just change how those files are picked up and passed to the module).

Yes that's my plan for multi-module database construction commands (e.g. kraken2), or do you have a motivation to do this for single build modules too?

No, I don't see a reason for single modules. I didn't read the file properly and somehow thought the input channel transformation was Kaiju-specific.

Ah ok! Then I leave that bit as is for now at least.

[jfy133]

OK thank you for the reviews @maxulysse @Joon-Klaps @Midnighter !

I've addressed all the suggestions now (except for the larger one from @Midnighter regarding taxdump, but I'll do that as a follow up), so I will merge so others can start to get involved, and other unaddressed changes can be dealt with in a follow up :)