FEAT: Release Canditate 3.3.2 #1264

maxulysse · 2023-09-29T12:42:45Z

Replace #1263

PR checklist

back to dev

fix result path

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

FIX: remove spaces in controlfreec modules

Co-authored-by: Friederike Hanssen <[email protected]>

FEAT: Improve documentation for annotation cache

Add nf-prov

Co-authored-by: Friederike Hanssen <[email protected]>

FEAT: add merge to cache checks

github-actions · 2023-09-29T12:44:44Z

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

Posted for pipeline commit fabd58b

+| ✅ 146 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.3.2
pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ 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

✅ 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: 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-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_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: ci.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-announcments.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 2023-10-04 07:51:21

FEAT: prepare RC 3.3.2

CHANGELOG.md

workflows/sarek.nf

FIX: revert controlfreec-assesssignificance

JoseEspinosa

LGTM!

FriederikeHanssen and others added 30 commits September 18, 2023 18:59

back to dev

6bf5561

Merge pull request #1246 from FriederikeHanssen/backtodev

64a8e36

back to dev

fix result path

1b1d24c

Merge pull request #1247 from FriederikeHanssen/fix_paths

4f0d65a

fix result path

better docs

aaaf953

more safeguards

0de1049

update WEBSITE

90d5bc8

Template update for nf-core/tools version 2.10

75fc5ca

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

885ebf6

merge leftovers

f7f34b3

merge leftovers

855393e

typo

a96508f

fix multiqc linting comments

986ed6e

Merge pull request #1254 from nf-core/nf-core-template-merge-2.10

96140de

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

update CHANGELOG

55085a5

better docs

87b83c8

update controlfreec modules

1d218b4

update CHANGELOG

f3314b8

Merge pull request #1256 from maxulysse/controlfreec

f1dfdac

FIX: remove spaces in controlfreec modules

better error handling when no cache provided

8cbbf97

forgot a case in the if else logic

0f36b8a

unhide some params

a7acd5c

Update docs/usage.md

544e16c

Co-authored-by: Friederike Hanssen <[email protected]>

Apply suggestions from code review

bd1748b

Apply suggestions from code review

5898739

point towards correct docs

9e3e91d

Merge pull request #1248 from maxulysse/annotation_cache_docs

4cb2c2a

FEAT: Improve documentation for annotation cache

add nf-prov

cb14579

update CHANGELOG

96f4f20

add merge to cache checks

a7ada18

maxulysse and others added 6 commits September 29, 2023 12:01

Merge pull request #1259 from maxulysse/nf-prov

ffda6bb

Add nf-prov

split was useful

1ab6ff8

Update CHANGELOG.md

50747d6

Co-authored-by: Friederike Hanssen <[email protected]>

Merge pull request #1261 from maxulysse/annotation_merge

28f9077

FEAT: add merge to cache checks

FEAT: prepare RC 3.3.2

dd76ebf

prettier

9aebc2d

Merge pull request #1262 from maxulysse/prepare-rc-3_3_2

b043eee

FEAT: prepare RC 3.3.2

maxulysse commented Sep 29, 2023

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maxulysse commented Sep 29, 2023

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maxulysse commented Sep 29, 2023

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Apply suggestions from code review

1cb015a

maxulysse commented Oct 1, 2023

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maxulysse commented Oct 1, 2023

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maxulysse added 5 commits October 1, 2023 19:42

Apply suggestions from code review

1527364

revert controlfreec-assesssignificance

fa212b2

update CHANGELOG

547a1a4

update dependencies table

b84b8b5

Merge pull request #1270 from maxulysse/asses_significance

fabd58b

FIX: revert controlfreec-assesssignificance

JoseEspinosa approved these changes Oct 4, 2023

View reviewed changes

FriederikeHanssen approved these changes Oct 4, 2023

View reviewed changes

maxulysse merged commit f034b73 into master Oct 4, 2023
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FEAT: Release Canditate 3.3.2 #1264

FEAT: Release Canditate 3.3.2 #1264

maxulysse commented Sep 29, 2023

github-actions bot commented Sep 29, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

FEAT: Release Canditate 3.3.2 #1264

FEAT: Release Canditate 3.3.2 #1264

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maxulysse commented Sep 29, 2023

PR checklist

github-actions bot commented Sep 29, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

JoseEspinosa left a comment

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github-actions bot commented Sep 29, 2023 •

edited

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