Candidate release 3.3.1 #1244

FriederikeHanssen · 2023-09-18T14:40:07Z

PR checklist

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

Back to dev

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

Fix Zenodo ID in manifest

FIX: remove check annotation folders existence when no annotation

FIX: Disable JVM hotspot in gatk4 modules

…nto dev

Update controlfreec version

FEAT: Improve schema usage for input

Simplify sentieon test license server usage

CHANGELOG.md

github-actions · 2023-09-18T14:42:20Z

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

Posted for pipeline commit 8785be8

+| ✅ 142 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.3.1

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_ci - actions_ci
template_strings - template_strings
multiqc_config - multiqc_config

✅ 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-sarek_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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: lib/WorkflowSarek.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-sarek_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 - 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_awstest - '.github/workflows/awstest.yml' is triggered correctly
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: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.9
Run at 2023-09-18 15:38:24

nextflow.config

maxulysse

missing a bump version + codename

maxulysse

#1245 will cover the requested changes

jfy133

Simple enough!

CHANGELOG.md

modules/nf-core/controlfreec/makegraph/meta.yml

workflows/sarek.nf

prepare release

asp8200 and others added 30 commits September 14, 2023 07:30

back to dev

33cbc82

Fix PR number

2e6c1b9

Update CHANGELOG.md

24f3dfe

Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

[automated] Fix linting with Prettier

d22d60b

Merge pull request #1231 from asp8200/prepare_release_3_4

8c167bf

Back to dev

Fix Zenodo ID in manifest

0f8a8b3

Update nextflow.config

578ac62

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

update to v2

b0494a8

remove v2

1ede558

Merge pull request #1232 from FriederikeHanssen/zenodo

a0c0cbd

Fix Zenodo ID in manifest

update CHANGELOG

b2dde77

fixing folder checks

15206c9

add meta map to channel

841ed94

more complete error message

09553a7

fix map

9e27d77

simplify logic

0918d31

remove usage of sentieon secrets in cache.config

a3d57b4

introducing profile sentieon_test_licence

bede8ab

more safeguards

ed0e052

code polish

e745db6

Merge pull request #1236 from maxulysse/fix_annotation_unused

c6ec5dc

FIX: remove check annotation folders existence when no annotation

Forgot profile sentieon_test_licence in some tests

137e2ca

update all gatk modules with disabling JVM hotspot fix

6827e45

update CHANGELOG

638538f

Fix typo in nf secrets cmd

a774c91

Update controlfreec version

6242c31

Merge pull request #1240 from maxulysse/gatk4_hotspot

35b42ce

FIX: Disable JVM hotspot in gatk4 modules

Merge branch 'dev' into update_freec

c070ea4

Merge branch 'sentieon-license-fixing2' of github.com:nf-core/sarek i…

3c568e7

…nto dev

use profile from configs

a55df91

maxulysse added 12 commits September 18, 2023 10:03

update CHANGELOG

2882b0c

forgot this test

0298c65

Merge pull request #1241 from FriederikeHanssen/update_freec

d50e63b

Update controlfreec version

improve schema json for input

ebf0897

update CHANGELOG

b1407ba

Merge pull request #1243 from nf-core/improve_nextflow_schema

607ecd6

FEAT: Improve schema usage for input

update tests

a071f26

renamed file

83da7c0

Merge branch 'dev' into sentieon-license-fixing3

8617e92

Apply suggestions from code review

56c1916

Update tests/test_umi.yml

c12ed5b

Merge pull request #1242 from nf-core/sentieon-license-fixing3

647b664

Simplify sentieon test license server usage

FriederikeHanssen requested a review from maxulysse as a code owner September 18, 2023 14:40

maxulysse reviewed Sep 18, 2023

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maxulysse reviewed Sep 18, 2023

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maxulysse requested changes Sep 18, 2023

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prepare release

10fccc6

maxulysse approved these changes Sep 18, 2023

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jfy133 approved these changes Sep 18, 2023

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workflows/sarek.nf Show resolved Hide resolved

FriederikeHanssen added 2 commits September 18, 2023 15:23

Add release name

176d292

Merge pull request #1245 from FriederikeHanssen/prepare_release_331

8785be8

prepare release

FriederikeHanssen merged commit 59026dc into master Sep 18, 2023

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Candidate release 3.3.1 #1244

Candidate release 3.3.1 #1244

FriederikeHanssen commented Sep 18, 2023

github-actions bot commented Sep 18, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

maxulysse left a comment

jfy133 left a comment

Candidate release 3.3.1 #1244

Candidate release 3.3.1 #1244

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FriederikeHanssen commented Sep 18, 2023

PR checklist

github-actions bot commented Sep 18, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse left a comment

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github-actions bot commented Sep 18, 2023 •

edited

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