Precomputed BUSCO [WIP] by tkchafin · Pull Request #135 · sanger-tol/blobtoolkit

tkchafin · 2025-02-19T16:26:27Z

Not completed/ not ready for review

PR checklist

Updated BTK container to ensure the right Busco ID is used

github-actions · 2025-03-03T10:25:27Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit f8e019b

+| ✅ 128 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 0.7.0
schema_description - Ungrouped param in schema: busco_output

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/igenomes.config
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/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/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 ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
template_strings - template_strings
merge_markers - merge_markers

✅ 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: 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/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: lib/nfcore_external_java_deps.jar
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.yml
files_exist - File found: conf/base.config
files_exist - File found: lib/WorkflowBlobtoolkit.groovy
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-blobtoolkit_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: .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 params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
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 - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar 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 Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
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: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
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 2.11
Run at 2025-03-03 14:08:29

tkchafin and others added 13 commits February 19, 2025 12:38

accepts pre-computed busco as param

bc183c4

generate_config works with precomp buscos

27da84e

fixed generate_config with or without precomp busco

f944a34

almost there

42cb2c1

working for precomputed, not without...

2e5b487

now working for precomp, non-precomp, and mixed busco outputs

a224fad

Updated BTK container to ensure the right Busco ID is used

f5e890a

upload-artifact bump

e33ca14

Merge pull request sanger-tol#139 from sanger-tol/busco_bug_full_test

3f450fd

Updated BTK container to ensure the right Busco ID is used

Delete busco_output directory

038e4f5

upload-artifact@v4

b6181e9

python-black linting

da32d92

Merge branch 'sanger-tol:dev' into dev

3652256

tkchafin added 3 commits March 3, 2025 14:01

precom busco documentation

a29bc67

prettier linting

df44525

prettier linting

f8e019b

tkchafin requested a review from muffato March 3, 2025 15:02

tkchafin merged commit d9aaea9 into sanger-tol:precomp_busco Mar 3, 2025
6 checks passed

muffato added this to the v0.7.0 milestone Feb 20, 2026

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Precomputed BUSCO [WIP]#135

Precomputed BUSCO [WIP]#135
tkchafin merged 16 commits intosanger-tol:precomp_buscofrom
tkchafin:dev

tkchafin commented Feb 19, 2025 •

edited

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github-actions bot commented Mar 3, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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tkchafin commented Feb 19, 2025 •

edited

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github-actions bot commented Mar 3, 2025 •

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`nf-core lint` overall result: Passed ✅ ⚠️