Update/dbs download

[Ales-ibt]

Hello! This is an update to the pipeline to function with any catalogue we have available in MGnify.
Thank you for taking a look.

[mberacochea]

Thank you @Ales-ibt. I think we need to migrate the DB downloading bits into the pipeline (as nextflow subworkflows). I'll add this to our next sprint... so don't worry about it.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b250809

+| ✅ 123 tests passed       |+
#| ❔  48 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes_ignored.config
• files_exist - File not found: .github/workflows/awstest.yml
• files_exist - File not found: .github/workflows/awsfulltest.yml
• files_exist - File not found: ro-crate-metadata.json
• nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
• nextflow_config - Config manifest.version should end in dev: 1.1.0
• pipeline_todos - TODO string in WorkflowShallowmapping.groovy: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
• pipeline_todos - TODO string in ci.yml.bak: You can customise CI pipeline run tests as required
• 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-shallowmapping_logo_light.png
• files_exist - File is ignored: docs/
• 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: docs/images/nf-core-shallowmapping_logo_dark.png
• files_exist - File is ignored: docs/images/nf-core-shallowmapping_logo_light.png
• files_exist - File is ignored: pyproject.toml
• files_exist - File is ignored: .gitignore
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/*
• files_exist - File is ignored: .github/workflows/branch.yml
• files_exist - File is ignored: .github/CONTRIBUTING.md
• files_exist - File is ignored: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/test.config
• files_exist - File is ignored: conf/test_full.config
• 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/WorkflowShallowmapping.groovy
• files_exist - File is ignored: lib/nfcore_external_java_deps.jar
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config variable ignored: process.cpus
• nextflow_config - Config variable ignored: process.memory
• nextflow_config - Config variable ignored: process.time
• nextflow_config - Config variable ignored: params.max_cpus
• 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/CONTRIBUTING.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/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .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/nf-core-shallowmapping_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-shallowmapping_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-shallowmapping_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_ci - '.github/workflows/ci.yml' not found
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/shallowmapping/shallowmapping/.github/workflows/awstest.yml

✅ Tests passed:

• files_exist - File found: .gitattributes
• 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/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.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: 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-shallowmapping_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: .travis.yml
• nextflow_config - Found nf-validation plugin
• 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: params.outdir
• nextflow_config - Config variable found: params.input
• 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.outdir= results
• 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/ISSUE_TEMPLATE/feature_request.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
• readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description 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.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: release-announcments.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 - ALIGN_BWAMEM2 found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTP found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - SOURMASH_GATHER found in conf/modules.config and Nextflow scripts.
• modules_config - ALIGN_BWAMEM2 found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_SOURMASHTAXO found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_BWATAXO found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_FUNCTIONSPRED found in conf/modules.config and Nextflow scripts.
• modules_config - DRAM_DISTILL found in conf/modules.config and Nextflow scripts.
• modules_config - KEGG_COMPLETENESS found in conf/modules.config and Nextflow scripts.
• modules_config - KEGG_SPECIES found in conf/modules.config and Nextflow scripts.
• modules_config - POSTPROC_INTEGRATOR found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS 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 3.1.0
• Run at 2024-12-17 16:34:35