Added CI tests for SpeciesAbundance workflow pipeline

[kylacochrane]

This PR adds CI testing to the GitHub Actions (ci.yml), and to the pipeline as a whole: tests/main.nf.test

• the workflow pipeline (speciesabundance.nf) was updated to accommodate additional testing
• the test database was separated into two separate directories to expand testing options (now called krakendatabase and brackendatabase, where corresponding files can be found that are accessed by each module).

Various config files were updated accordingly:

• nextflow.config
• nextflow_schema.json
• nf-test.config
• conf/test.config

The branch has also been tested in Azure.

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!
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit dd6bd99

+| ✅ 125 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

• schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/speciesabundance/master/nextflow_schema.json
  Found https://raw.githubusercontent.com/phac-nml/speciesabundance/main/nextflow_schema.json

❔ Tests ignored:

• files_exist - File is ignored: assets/nf-core-speciesabundance_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-speciesabundance_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-speciesabundance_logo_dark.png
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: lib/Utils.groovy
• files_exist - File is ignored: lib/WorkflowMain.groovy
• files_exist - File is ignored: lib/NfcoreTemplate.groovy
• files_exist - File is ignored: lib/WorkflowSpeciesabundance.groovy
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• 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 ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.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 ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File does not exist: assets/nf-core-speciesabundance_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-speciesabundance_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-speciesabundance_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/speciesabundance/speciesabundance/.github/workflows/awstest.yml
• actions_awsfulltest - actions_awsfulltest
• pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.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: 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/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/ci.yml
• 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/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: modules.json
• files_exist - File found: pyproject.toml
• files_exist - File not found check: Singularity
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: .nf-core.yaml
• 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: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: docs/images/nf-core-speciesabundance_logo.png
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: params.validationShowHiddenParams
• nextflow_config - Config variable found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 1.0.0dev
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.taxonomic_level= S
• nextflow_config - Config default value correct: params.max_cpus= 4
• nextflow_config - Config default value correct: params.max_memory= 2.GB
• nextflow_config - Config default value correct: params.max_time= 1.h
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.validate_params= true
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• files_unchanged - pyproject.toml matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• template_strings - Did not find any Jinja template strings (89 files)
• schema_lint - Schema lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - 'assets/multiqc_config.yml' contains report_section_order
• multiqc_config - 'assets/multiqc_config.yml' contains export_plots
• multiqc_config - 'assets/multiqc_config.yml' contains report_comment
• multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
• multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

• nf-core/tools version 2.13.1
• Run at 2024-04-03 17:29:36

[apetkau]

This is amazing. Thanks so much for all your hard work Kyla 😄 🐙 🥬

I still have to test this out on my computer, but I have comments below.

[apetkau]

This looks great to me. Thanks so much Kyla.

[emarinier]

Looks good. Just a few small comments.