Add --average-method parameter to autometa-benchmark

[evanroyrees]

• fixes-Add average_method argument to compute_clustering_metrics function #289
• 🎨🐍 Add --average-method arg to autometa-benchmark
• 🎨 Add average_method arg to evaluate_clustering(..., average_method)
• 🎨 Add average_method arg to compute_clustering_metrics(..., average_method)

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 646a146

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

❗ Test warnings:

• readme - README did not have a Nextflow minimum version badge.
• readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
• schema_lint - 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 - No description provided in schema for parameter: plaintext_email
• schema_description - No description provided in schema for parameter: custom_config_version
• schema_description - No description provided in schema for parameter: custom_config_base
• schema_description - No description provided in schema for parameter: hostnames
• schema_description - No description provided in schema for parameter: show_hidden_params
• schema_description - No description provided in schema for parameter: singularity_pull_docker_container

❔ Tests ignored:

• files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File is ignored: .github/workflows/branch.yml
• files_exist - File is ignored: .github/workflows/ci.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: assets/nf-core-autometa_logo_light.png
• files_exist - File is ignored: docs/usage.md
• files_exist - File is ignored: docs/output.md
• files_exist - File is ignored: docs/images/nf-core-autometa_logo.png
• files_exist - File is ignored: docs/images/nf-core-autometa_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-autometa_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.md
• nextflow_config - nextflow_config
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File does not exist: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/email_template.html
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File does not exist: assets/nf-core-autometa_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-autometa_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-autometa_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
• files_unchanged - File ignored due to lint config: .gitignore or foo
• actions_ci - '.github/workflows/ci.yml' not found
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/Autometa/Autometa/.github/workflows/awstest.yml
• template_strings - template_strings

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .markdownlint.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: lib/nfcore_external_java_deps.jar
• files_exist - File found: lib/NfcoreSchema.groovy
• files_exist - File found: lib/NfcoreTemplate.groovy
• files_exist - File found: lib/Utils.groovy
• files_exist - File found: lib/WorkflowMain.groovy
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yaml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: lib/WorkflowAutometa.groovy
• files_exist - File found: modules.json
• files_exist - File not found check: Singularity
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .travis.yml
• files_unchanged - .gitattributes matches the template
• files_unchanged - .markdownlint.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - lib/nfcore_external_java_deps.jar matches the template
• files_unchanged - lib/NfcoreSchema.groovy matches the template
• files_unchanged - assets/multiqc_config.yaml matches the template
• pipeline_name_conventions - Name adheres to nf-core convention
• schema_lint - Schema lint passed
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: docker_mock_data_reporter.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: pytest_codecov.yml
• actions_schema_validation - Workflow validation passed: docker_get_genomes_for_mock.yml
• actions_schema_validation - Workflow validation passed: docker_autometa.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json

Run details

• nf-core/tools version 2.2
• Run at 2022-09-22 18:54:57

[codecov]

Codecov Report

Base: 27.35% // Head: 27.62% // Increases project coverage by +0.27% 🎉

Coverage data is based on head (ad0efd0) compared to base (9772257).
Patch coverage: 0.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #290      +/-   ##
==========================================
+ Coverage   27.35%   27.62%   +0.27%     
==========================================
  Files          50       50              
  Lines        5733     5734       +1     
==========================================
+ Hits         1568     1584      +16     
+ Misses       4165     4150      -15     

Flag	Coverage Δ
unittests	27.62% <0.00%> (+0.27%)	⬆️

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

Impacted Files	Coverage Δ
autometa/validation/benchmark.py	0.00% <0.00%> (ø)
autometa/binning/unclustered_recruitment.py	91.89% <0.00%> (+8.64%)	⬆️

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