1.1.2 release #411

jfy133 · 2023-10-27T03:13:54Z

Bug fixes release 1.1.2!

PR checklist

bump version

Kaiju2krona fix

…g steps

Add preprint citation info

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

…on-fix Disambiguate same-db name but bracken step kraken from profile mergin…

Megan container update

github-actions · 2023-10-27T03:16:15Z

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

Posted for pipeline commit 73ec485

+| ✅ 158 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.2
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ 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: 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: assets/nf-core-taxprofiler_logo_light.png
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/images/nf-core-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_logo_dark.png
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: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowTaxprofiler.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-taxprofiler_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.name
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: manifest.homePage
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 manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
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
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml 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 - .github/workflows/linting.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
files_unchanged - assets/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy 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
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
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 (206 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcments.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' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
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 2.10
Run at 2023-10-27 05:39:28

Release version bump

subworkflows/local/standardisation_profiles.nf

sofstam

🚀

LilyAnderssonLee and others added 23 commits October 11, 2023 16:08

bump version

1712c0a

Update nextflow.config

785b8f0

Apply suggestions from code review

ca73d4d

Merge pull request #402 from LilyAnderssonLee/bump_version

bdf88d2

bump version

Fix KAIJU2KRONA input tool/db mismatch

936528a

Tweak changelgo

8245980

Merge pull request #405 from nf-core/kaiju2krona-fix

067cd2c

Kaiju2krona fix

Disambiguate same-db name but bracken step kraken from profile mergin…

25a80a2

…g steps

Add final docs

f87ed97

Update changelgo

51cf6be

Merge branch 'dev' into krona-ktimporttext-input-collision-fix

bdd514d

Add preprint citation info

c5582aa

Update README.md

16b8157

Update CHANGELOG.md

6282a69

Merge pull request #408 from nf-core/preprint-citations

f18df85

Add preprint citation info

Apply suggestions from code review

da8bf5a

Co-authored-by: Moritz E. Beber <midnighter@posteo.net>

Merge pull request #406 from nf-core/krona-ktimporttext-input-collisi…

267e1a1

…on-fix Disambiguate same-db name but bracken step kraken from profile mergin…

Update MEGAN

527ca85

Update CHANGELOG

06d4360

Update Changelog

aa4e916

Add PR links in CHANGELOG

1986520

Add missing modules.json update

c22f719

Merge pull request #409 from nf-core/megan-update

0805d06

Megan container update

jfy133 added the WIP Work in progress label Oct 27, 2023

jfy133 marked this pull request as draft October 27, 2023 03:14

Release version bump

e27ac82

jfy133 added 2 commits October 27, 2023 06:44

Update CHANGELOG.md

32d0d6e

Merge pull request #412 from nf-core/bump-version-for-release

73ec485

Release version bump

jfy133 marked this pull request as ready for review October 27, 2023 05:37

jfy133 removed the WIP Work in progress label Oct 27, 2023

jfy133 requested a review from a team October 27, 2023 05:38

matthdsm approved these changes Oct 27, 2023

View reviewed changes

sofstam reviewed Oct 27, 2023

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subworkflows/local/standardisation_profiles.nf Show resolved Hide resolved

sofstam self-requested a review October 27, 2023 07:28

sofstam approved these changes Oct 27, 2023

View reviewed changes

jfy133 merged commit 3d4eda2 into master Oct 27, 2023

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1.1.2 release #411

1.1.2 release #411

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jfy133 commented Oct 27, 2023

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1.1.2 release #411

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jfy133 commented Oct 27, 2023

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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github-actions bot commented Oct 27, 2023 •

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