Add CITATION file

[shaneroesemann]

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/autometa 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).
• [ ] 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 eb29f23

+| ✅  62 tests passed       |+
#| ❔  34 tests were ignored |#
!| ❗   9 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version badge. * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README did not have a Nextflow minimum version mentioned in Quick Start section. * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema `$id` should be `https://raw.githubusercontent.com/autometa/master/nextflow_schema.json` Found `https://raw.githubusercontent.com/autometa/main/nextflow_schema.json` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `plaintext_email` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `custom_config_version` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `custom_config_base` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `hostnames` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `show_hidden_params` * [schema_description](https://nf-co.re/tools-docs/lint_tests/schema_description.html) - No description provided in schema for parameter: `singularity_pull_docker_container` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-autometa_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/usage.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/output.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-autometa_logo.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-autometa_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-autometa_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/feature_request.md` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - nextflow_config * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/CONTRIBUTING.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/PULL_REQUEST_TEMPLATE.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `.github/workflows/branch.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/linting_comment.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/linting.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `assets/email_template.html` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `assets/email_template.txt` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/nf-core-autometa_logo_light.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-autometa_logo_light.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-autometa_logo_dark.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `docs/README.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `lib/NfcoreTemplate.groovy` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.gitignore` or `foo` * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' not found * [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - 'awstest.yml' workflow not found: `/home/runner/work/Autometa/Autometa/.github/workflows/awstest.yml` * [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - template_strings ### :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: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreSchema.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `main.nf` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/multiqc_config.yaml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowAutometa.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `modules.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.travis.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.markdownlint.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreSchema.groovy` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/multiqc_config.yaml` matches the template * [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema lint passed * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: docker_get_genomes_for_mock.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: docker_mock_data_reporter.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: pytest_codecov.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: docker_autometa.yml * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json` ### Run details * nf-core/tools version 2.2 * Run at `2022-02-27 15:42:52`

[codecov[bot]]

Codecov Report

Merging #242 (eb29f23) into main (ad0364a) will decrease coverage by 0.29%. The diff coverage is n/a.

@@            Coverage Diff             @@
##             main     #242      +/-   ##
==========================================
- Coverage   27.61%   27.31%   -0.30%     
==========================================
  Files          45       45              
  Lines        5334     5334              
==========================================
- Hits         1473     1457      -16     
- Misses       3861     3877      +16     

Flag	Coverage Δ
unittests	27.31% <ø> (-0.30%)	:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
autometa/binning/unclustered_recruitment.py	83.15% <0.00%> (-8.70%)	:arrow_down:

---

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Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update ad0364a...eb29f23. Read the comment docs.

[shaneroesemann]

happy to make the branch change.

title: Autometa
authors: 
  - family-names: Kwan
    given-names: Jason C.

^^ this needed to be included. At least through the context of validating the .cff with cffconvert. I originally did not have it but the validation required a title and author field in the first indentation. Maybe I can look into validating it on my personal github and/or look into a different validation package (i see there is at least one other).

I can make the changes you suggested, thanks

[shaneroesemann]

@chasemc @WiscEvan
OK I made the changes requested. I think I pushed to the dev branch this time. thanks

[chasemc]

Looks good, I checked it in another repo and it shows the citation as the v1 manuscript I changed the PR to merge into dev

[chasemc]

@WiscEvan I don't get why codecov is picking up on an unchanged file?

[evanroyrees]

@WiscEvan I don't get why codecov is picking up on an unchanged file?

I'm not sure why codecov is picking this up. It has shown some odd behavior in the past 🤷