Release PR for 1.1.4 #316

jasmezz · 2023-11-07T08:47:22Z

See changelog

PR checklist

Post-release version bump

Fix deepARG test profile and use more stable deepARG db URL

This reverts commit 837442a.

Stop `prokka` from renaming contigs by default

Important! Template update for nf-core/tools v2.10

Modules updates: Bakta, AMRFinderPlus, and MultiQC

fix input schema to accept uncompressed fasta; fix #309

Co-authored-by: Louisa Perelo <[email protected]>

Release version bump to 1.1.4

github-actions · 2023-11-07T08:49:49Z

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

Posted for pipeline commit 86ba79b

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.1.4
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: 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-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 (153 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: branch.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.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 2023-11-07 08:49:30

docs/usage.md

nextflow_schema.json

CHANGELOG.md

Skip CI tests because only docs are updated (and previous CI tests succeeded) Co-authored-by: Matthias Hörtenhuber <[email protected]>

FriederikeHanssen

looks good, just wondering about the old multiqc version

CHANGELOG.md

jasmezz and others added 30 commits August 11, 2023 14:38

Post-release version bump

e736dd4

Update changelog

caaa682

stop prokka from renaming contigs by default

83ec5c7

CHANGELOG prettier

eaf4387

Fix new parameter

628111b

Fix deepARG test profile and use more stable deepARG db URL

bb8334c

Reduce deepARG test annotaion tool to prevent zenodo DL throttling

f651f88

Merge pull request #304 from nf-core/post-release_version_bump

ae78dad

Post-release version bump

Merge remote-tracking branch 'origin/dev' into stablish-deeparg

7fd4d3a

Update CHANBGELOG

edb6c97

Apply suggestions from code review

079ef0f

Add review requests

c749b5e

Add DeepARG Zenodo link to usage docs

b7c5237

Merge branch 'dev' into rename_contigs_prokka

69be59d

Update .github/workflows/ci.yml

bc4db0d

Merge pull request #307 from nf-core/stablish-deeparg

342b848

Fix deepARG test profile and use more stable deepARG db URL

Merge branch 'dev' into rename_contigs_prokka

4ea8310

Merge branch 'nf-core:master' into rename_contigs_prokka

fea43ba

Update amrfinderplus, bakta, and multiqc

2d1a2ec

Update changelog

837442a

Revert "Update changelog"

c56197f

This reverts commit 837442a.

Update changelog

d230766

Merge pull request #306 from Darcy220606/rename_contigs_prokka

e0635da

Stop `prokka` from renaming contigs by default

fix input schema to accept uncompressed fasta; fix #309

adaefa5

Template update for nf-core/tools version 2.10

b2ad76f

Merge branch 'dev' into nf-core-template-merge-2.10

7241c08

Remove duplicated import line in funcscan.nf

b5fc8cb

Apply suggestions from code review

8096f0a

Update amrfinderplus, fastqc

cd0f914

Comment out duplicate import line

e280177

jasmezz and others added 15 commits September 28, 2023 16:25

Remove fastqc

7228cd9

Remove duplicate import line [skip ci]

f08723f

Merge pull request #311 from nf-core/nf-core-template-merge-2.10

6cdd651

Important! Template update for nf-core/tools v2.10

Merge branch 'dev' into modules_update

5e7cc6b

Merge pull request #308 from nf-core/modules_update

522ca9d

Modules updates: Bakta, AMRFinderPlus, and MultiQC

Merge remote-tracking branch 'upstream/dev' into fix_gz

bd61a80

update changelog

a2b8802

Merge pull request #310 from tavareshugo/fix_gz

ffba284

fix input schema to accept uncompressed fasta; fix #309

Update version + changelog + metromap

61ba895

Update multiqc_config.yml

66a5fdc

Remove deepbgc CI tests

c4f0a54

Apply suggestions from code review

07fdae4

Co-authored-by: Louisa Perelo <[email protected]>

Fix .github/workflows/ci.yml

6aebacf

Update CHANGELOG.md [skip ci]

c84e720

Merge pull request #314 from nf-core/release-version-bump

86ba79b

Release version bump to 1.1.4

mashehu approved these changes Nov 7, 2023

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FriederikeHanssen reviewed Nov 7, 2023

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jasmezz commented Nov 7, 2023

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Apply suggestions from code review [skip ci]

85dae3f

Skip CI tests because only docs are updated (and previous CI tests succeeded) Co-authored-by: Matthias Hörtenhuber <[email protected]>

FriederikeHanssen reviewed Nov 7, 2023

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jasmezz commented Nov 7, 2023

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5c7aebf

jasmezz merged commit 274042b into master Nov 7, 2023
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Release PR for 1.1.4 #316

Release PR for 1.1.4 #316

jasmezz commented Nov 7, 2023

github-actions bot commented Nov 7, 2023

❗ Test warnings:

✅ Tests passed:

Run details

FriederikeHanssen left a comment

Release PR for 1.1.4 #316

Release PR for 1.1.4 #316

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jasmezz commented Nov 7, 2023

PR checklist

github-actions bot commented Nov 7, 2023

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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