Release PR for 1.1.3 #303

jasmezz · 2023-08-09T10:27:36Z

See changelog

PR checklist

…can into nf-core-template-merge-2.9

Co-authored-by: Jasmin Frangenberg <[email protected]>

Important! Template update for nf-core/tools v2.9

Version bump + changelog update

… screening

add Prokka to MultiQC

adding nf-core/validation

Update prodigal output filename pattern

Add QC check for empty files out of annotation

Co-authored-by: James A. Fellows Yates <[email protected]>

Modules update incl. fixing pigz in Pyrodigal

Fix pyrodigal channels, update ampcombi docs

Small updates to schema JSON to remove false and "None" defaults.

Release version bump 1.1.3

github-actions · 2023-08-09T10:29:43Z

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

Posted for pipeline commit 57e1533

+| ✅ 156 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.3
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-funcscan_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-funcscan_logo_light.png
files_exist - File found: docs/images/nf-core-funcscan_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/WorkflowFuncscan.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: .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-funcscan_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-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_logo_light.png matches the template
files_unchanged - docs/images/nf-core-funcscan_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 (154 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.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2.9
Run at 2023-08-11 07:21:41

jfy133

one-handed review featuring sleeping baby in my arm!

lib/WorkflowFuncscan.groovy

workflows/funcscan.nf

louperelo and others added 30 commits May 31, 2023 15:15

test nf-core validation

fc5008c

update parameter name

2e1b8e8

fix input file in schema

f18e87f

Template update for nf-core/tools version 2.9

6ed1161

Merge branch 'dev' into nf-core-template-merge-2.9

e3da140

Set fasta existance check to false

6484747

Update nxf versions across all CI tests

46fba73

Apply suggestions from code review

1680f8b

[automated] Fix linting with Prettier

4e65643

Add hamronization DOI + version bump

ab83848

Add a couple of missing citations and add full methods tesxt

4e1f08f

Merge branch 'nf-core-template-merge-2.9' of github.com:nf-core/funcs…

45673f1

…can into nf-core-template-merge-2.9

Update CITATIONS.md

df5af52

Co-authored-by: Jasmin Frangenberg <[email protected]>

Merge pull request #290 from nf-core/nf-core-template-merge-2.9

8073125

Important! Template update for nf-core/tools v2.9

Merge branch 'dev' into hamronization_doi

088d736

Update changelog

a55fe6a

Remove duplicate hamronization reference

ec9626b

Merge pull request #294 from nf-core/hamronization_doi

e46519a

Version bump + changelog update

add Prokka to MultiQC

ff839b9

Updated prodigal output filename pattern

c26cd56

Update changelog

f46c532

[automated] Fix linting with Prettier

7a69688

update changelog

e2a95fd

Merge branch 'dev' into prokka_mqc

746718a

[automated] Fix linting with Prettier

53cd340

Filter out annotation files that are empty to prevent failures during…

26f9073

… screening

Apply suggestions from code review

2eae640

Add test nothing

3eee081

Merge branch 'dev' into validation

e45d437

Fix schema

8b7de44

jfy133 and others added 25 commits July 19, 2023 11:37

Merge branch 'start-qc' of github.com:nf-core/funcscan into start-qc

a4b711e

Merge pull request #295 from louperelo/prokka_mqc

c61ea09

add Prokka to MultiQC

Apply suggestions from code review

18a9af4

Update CHANGELOG.md

2354a87

Merge pull request #285 from nf-core/validation

22f26b2

adding nf-core/validation

Merge branch 'dev' into start-qc

9d16c0d

Merge pull request #296 from nf-core/fix_prodigal_save_annotations

3bce3b4

Update prodigal output filename pattern

Merge pull request #297 from nf-core/start-qc

2a5c3ee

Add QC check for empty files out of annotation

Pull updated modules, adjust comBGC

ca9fb0d

Update changelog

d3d807f

Update changelog

21208ff

Update CHANGELOG.md

36fc195

Co-authored-by: James A. Fellows Yates <[email protected]>

Merge pull request #299 from nf-core/modules-update

fadc05c

Modules update incl. fixing pigz in Pyrodigal

Fix pyrodigal channels, update ampcombi docs

31269c4

Update changelog

288935d

Update changelog

751fa03

Merge pull request #300 from nf-core/fix_antismash_ampcombi

1e3649e

Fix pyrodigal channels, update ampcombi docs

Release version bump

23c8059

Switch off deeparg ci tests

7c2f8d2

Small updates to schema JSON to remove false and "None" defaults.

2b76c10

Update CHANGELOG.md [skip ci]

f82777d

Merge pull request #302 from nf-core/remove-none-from-schema

0cc3d5a

Small updates to schema JSON to remove false and "None" defaults.

Merge branch 'dev' into release-version-bump

844da36

Update changelog [skip ci]

73b1b15

Merge pull request #301 from nf-core/release-version-bump

352f979

Release version bump 1.1.3

jfy133 approved these changes Aug 10, 2023

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jasmezz added 2 commits August 11, 2023 09:20

Apply suggestions from code review

57e1533

Add correct date in changelog [skip ci]

0e3d179

jasmezz merged commit eb8f79c into master Aug 11, 2023
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Release PR for 1.1.3 #303

Release PR for 1.1.3 #303

jasmezz commented Aug 9, 2023

github-actions bot commented Aug 9, 2023 •

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❗ Test warnings:

✅ Tests passed:

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jfy133 left a comment

Release PR for 1.1.3 #303

Release PR for 1.1.3 #303

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jasmezz commented Aug 9, 2023

PR checklist

github-actions bot commented Aug 9, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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github-actions bot commented Aug 9, 2023 •

edited

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