1.1.4 Patch release #435

sofstam · 2024-01-24T10:29:10Z

PR checklist

Post release version bump

Fix the multiple fastq outputs in LONGREAD_HOSTREMOVAL

Update kaiju2table module

Bump version for patch release 1.1.4

github-actions · 2024-01-24T10:31:11Z

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

Posted for pipeline commit 9fd1446

+| ✅ 163 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.4

✅ Tests passed:

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files_exist - File found: CHANGELOG.md
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files_exist - File found: .github/.dockstore.yml
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files_exist - File found: lib/WorkflowTaxprofiler.groovy
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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/
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nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
files_unchanged - .gitattributes matches the template
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files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
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files_unchanged - .github/workflows/branch.yml matches the template
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files_unchanged - .github/workflows/linting.yml matches the template
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files_unchanged - assets/email_template.txt matches the template
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files_unchanged - docs/README.md matches the template
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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
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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
template_strings - Did not find any Jinja template strings (242 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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
merge_markers - No merge markers found in pipeline files
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multiqc_config - 'assets/multiqc_config.yml' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
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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 2.11.1
Run at 2024-01-24 10:30:53

LilyAnderssonLee · 2024-01-25T08:49:50Z

LGTM!

jfy133 and others added 19 commits January 12, 2024 16:18

Post release version bump

80bd413

Merge pull request #428 from nf-core/post-release-bump

0e3fb4f

Post release version bump

fix the output of fastq in LONGREAD_HOSTREMOVAL

ea57403

add changelog

08a05e1

nf-core-bot to fix the linting

7f621b3

Update kaiju2table module

c1120ba

Prettier

e6b9b26

update the publishDir pattern for samtools/fastq

28c850f

Merge pull request #430 from nf-core/samtools_fastq

1f34a9a

Fix the multiple fastq outputs in LONGREAD_HOSTREMOVAL

Merge branch 'dev' into update_kaiju_module

f5ae280

Prettier

eb96105

Prettier

761ba5b

[automated] Fix linting with Prettier

bd22884

Prettier

f5f5670

Prettier

10c4fad

Update all kaiju modules

913a2d7

Merge pull request #432 from genomic-medicine-sweden/update_kaiju_module

c301bd9

Update kaiju2table module

Patch release 1.1.4

47978b7

Merge pull request #434 from genomic-medicine-sweden/update_kaiju_module

9fd1446

Bump version for patch release 1.1.4

jfy133 approved these changes Jan 24, 2024

View reviewed changes

sofstam requested a review from LilyAnderssonLee January 25, 2024 08:23

LilyAnderssonLee approved these changes Jan 25, 2024

View reviewed changes

sofstam merged commit 21e6af8 into master Jan 25, 2024

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1.1.4 Patch release #435

1.1.4 Patch release #435

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sofstam commented Jan 24, 2024

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github-actions bot commented Jan 24, 2024 •

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LilyAnderssonLee commented Jan 25, 2024

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1.1.4 Patch release #435

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sofstam commented Jan 24, 2024

PR checklist

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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LilyAnderssonLee commented Jan 25, 2024

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github-actions bot commented Jan 24, 2024 •

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