Add more instructions now nextflow run.

[mberacochea]

I added the -latest flag for the nextflow run command and included additional documentation on running the pipeline.

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 63943db

+| ✅ 158 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 1.3
• pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
• schema_lint - Schema $schema should be http://json-schema.org/draft-07/schema
  Found https://json-schema.org/draft-07/schema
• system_exit - System.exit in main.nf: System.exit(1) [line 47]
• nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: CHANGELOG.md
• files_exist - File is ignored: assets/nf-core-mettannotator_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mettannotator_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mettannotator_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: conf/test_full.config
• files_exist - File is ignored: docs/output.md
• files_exist - File is ignored: docs/README.md
• files_exist - File is ignored: docs/usage.md
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: .github/workflows/ci.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/WorkflowMettannotator.groovy
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• 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/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/nf-core-mettannotator_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-mettannotator_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-mettannotator_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mettannotator/mettannotator/.github/workflows/awstest.yml

✅ 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: CITATIONS.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/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/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: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: modules.json
• 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: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• 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: docs/images/nf-core-mettannotator_logo.png
• 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: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• 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 - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.interproscan_db_version= 5.62-94.0
• nextflow_config - Config default value correct: params.interpro_entry_list_version= 94
• nextflow_config - Config default value correct: params.eggnog_db_version= 5.0.2
• nextflow_config - Config default value correct: params.rfam_ncrna_models_rfam_version= 14.9
• nextflow_config - Config default value correct: params.amrfinder_plus_db_version= 2024-01-31.1
• nextflow_config - Config default value correct: params.defense_finder_db_version= 1.2.3
• nextflow_config - Config default value correct: params.antismash_db_version= 7.1.0
• nextflow_config - Config default value correct: params.dbcan_db_version= 4.1.3_V12
• nextflow_config - Config default value correct: params.bakta_db_version= 2024-01-19
• nextflow_config - Config default value correct: params.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 128.GB
• nextflow_config - Config default value correct: params.max_time= 240.h
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• 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/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt 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 Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (131 files)
• schema_lint - Schema lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: pytest_ci.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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 found and not ignored.
• 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'
• base_config - conf/base.config found and not ignored.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• base_config - GECCO_RUN found in conf/base.config and Nextflow scripts.
• base_config - SANNTIS found in conf/base.config and Nextflow scripts.
• base_config - PROKKA found in conf/base.config and Nextflow scripts.
• base_config - EGGNOG_MAPPER found in conf/base.config and Nextflow scripts.
• base_config - INTERPROSCAN found in conf/base.config and Nextflow scripts.
• base_config - UNIFIRE found in conf/base.config and Nextflow scripts.
• base_config - DBCAN found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - QUAST found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/modules.config and Nextflow scripts.
• modules_config - CRISPRCAS_FINDER found in conf/modules.config and Nextflow scripts.
• modules_config - DETECT_TRNA found in conf/modules.config and Nextflow scripts.
• modules_config - DETECT_NCRNA found in conf/modules.config and Nextflow scripts.
• modules_config - ANTISMASH found in conf/modules.config and Nextflow scripts.
• modules_config - GECCO_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - SANNTIS found in conf/modules.config and Nextflow scripts.
• modules_config - UNIFIRE found in conf/modules.config and Nextflow scripts.
• modules_config - EGGNOG_MAPPER found in conf/modules.config and Nextflow scripts.
• modules_config - INTERPROSCAN found in conf/modules.config and Nextflow scripts.
• modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
• modules_config - BAKTA_BAKTA found in conf/modules.config and Nextflow scripts.
• modules_config - DBCAN found in conf/modules.config and Nextflow scripts.
• modules_config - ANNOTATE_GFF found in conf/modules.config and Nextflow scripts.
• modules_config - CIRCOS_PLOT found in conf/modules.config and Nextflow scripts.
• modules_config - DEFENSE_FINDER found in conf/modules.config and Nextflow scripts.
• modules_config - AMRFINDER_PLUS found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

• nf-core/tools version 2.14.1
• Run at 2024-11-20 14:58:15

[tgurbich]

Other than that, looks great, thanks a lot @mberacochea!