Workflow

[mattheww95]

Merging the initial workflow with some test data. The PR is being made so that the test data ends up in the correct place.

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @mattheww95,

It looks like this pull-request is has been made against the phac-nml/gasnomenclature main branch.
The main branch on phac-nml repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the phac-nml/gasnomenclature dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0cef238

+| ✅ 131 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

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

❔ Tests ignored:

• files_exist - File is ignored: assets/nf-core-gasnomenclature_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_dark.png
• files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_light.png
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• 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-gasnomenclature_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/gasnomenclature/gasnomenclature/.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-gasnomenclature_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/Utils.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/WorkflowGasnomenclature.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: v0.0.1dev
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.project_name= assembly
• nextflow_config - Config default value correct: params.assembler= stub
• nextflow_config - Config default value correct: params.random_seed= 1
• 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 (79 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: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.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 2024-04-02 19:50:07