Release 3.0.0 #447

rannick · 2023-11-24T14:47:02Z

PR checklist

bump version to 3.0.0

…usion into remove_squid_pizzly

…/rnafusion into collectinsertsizemetrics

Fix trim multiqc

update fusionreport

into add_positions_vcf

Add positions vcf

update doc

github-actions · 2023-11-24T14:48:34Z

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

Posted for pipeline commit 4ae96ff

+| ✅ 157 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
nextflow_config - Config manifest.version should end in dev: 3.0.0
pipeline_todos - TODO string in WorkflowRnafusion.groovy: Optionally add in-text citation tools to this list.

✅ 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-rnafusion_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-rnafusion_logo_light.png
files_exist - File found: docs/images/nf-core-rnafusion_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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowRnafusion.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-rnafusion_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-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_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 (234 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: release-announcments.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.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 2023-11-27 15:39:34

CHANGELOG.md

Co-authored-by: Alexander Peltzer <[email protected]>

fevac

🚀

nextflow.config

tower.yml

assets/multiqc_config.yml

CHANGELOG.md

Co-authored-by: Eva C <[email protected]>

rannick and others added 30 commits September 25, 2023 11:00

Merge pull request #405 from nf-core/bump_to_3.0.0

e3be022

bump version to 3.0.0

Merge branch 'dev' into tools_cutoff

c23a6ca

update modules.config

889df95

update changelog

f7fe23a

Merge branch 'dev' into remove_squid_pizzly

c7095ba

prettify

80b6347

Merge branch 'remove_squid_pizzly' of https://github.com/nf-core/rnaf…

41ae6b8

…usion into remove_squid_pizzly

Merge branch 'dev' into markduplicates_gatk4

65de953

Template update for nf-core/tools version 2.10

3187331

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

e7f5ffa

prettify

0cd1444

update modules and fix linting

1ad4190

remove trailing whitespace

8bc032f

correct pr mixup

5fe5b7f

update changelog

17dc46d

update multiqc config

62f0ffc

fix channel i/o and tower report path

0043c1f

Merge branch 'dev' into exchange_qualimap_with_mosdepth

9a36c85

Merge branch 'dev' into collectinsertsizemetrics

51c0744

update changelog

39d5eba

typo

7876dae

update changelog

eafe1b3

add to subworkflow

15e212d

Merge branch 'collectinsertsizemetrics' of https://github.com/nf-core…

b604fc3

…/rnafusion into collectinsertsizemetrics

replace qualimap with mosdepth in documentation, changelog

be96022

remove harsh trimming

be4e5ef

update changelog

5c35749

from megafusion to vcf_collect

1ea68bc

remove trim option

ca81a92

start collecting more information with vcf_collect

da68e1d

rannick added 14 commits November 24, 2023 14:46

Merge branch 'dev' into fix_trim_multiqc

2cb7fc5

Merge branch 'dev' into add_positions_vcf

8f0acc0

Merge pull request #440 from nf-core/fix_trim_multiqc

ba679fb

Fix trim multiqc

update fusionreport

635bee6

Merge branch 'dev' into update-fusionreport-no-fusiondgb

6007ea1

Merge pull request #445 from nf-core/update-fusionreport-no-fusiondgb

74f2f1a

update fusionreport

update changelog

4a216e7

Merge branch 'add_positions_vcf' of https://github.com/nf-core/rnafusion

323cf52

into add_positions_vcf

Merge branch 'dev' into add_positions_vcf

f5cc4a7

update doc

4596849

update changelof

a429ca8

merge

1ec2a29

Merge pull request #443 from nf-core/add_positions_vcf

d1bc30d

Add positions vcf

Merge pull request #446 from nf-core/update_weight_doc

ef99ba4

update doc

rannick self-assigned this Nov 24, 2023

rannick marked this pull request as ready for review November 24, 2023 15:12

apeltzer reviewed Nov 27, 2023

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apeltzer approved these changes Nov 27, 2023

View reviewed changes

Update CHANGELOG.md

df7a7b3

Co-authored-by: Alexander Peltzer <[email protected]>

fevac approved these changes Nov 27, 2023

View reviewed changes

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tower.yml Outdated Show resolved Hide resolved

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fevac reviewed Nov 27, 2023

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fevac reviewed Nov 27, 2023

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fevac reviewed Nov 27, 2023

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rannick and others added 5 commits November 27, 2023 16:12

Update tower.yml

c4526a9

Co-authored-by: Eva C <[email protected]>

bump version and remove igenomes param

cbf73a1

Merge branch 'dev' of https://github.com/nf-core/rnafusion into dev

bd82e62

update modules

89075bb

clarify changelog

4ae96ff

rannick merged commit f5ecf8d into master Nov 27, 2023
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Release 3.0.0 #447

Release 3.0.0 #447

rannick commented Nov 24, 2023

github-actions bot commented Nov 24, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

fevac left a comment

Release 3.0.0 #447

Release 3.0.0 #447

Conversation

rannick commented Nov 24, 2023

PR checklist

github-actions bot commented Nov 24, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

fevac left a comment

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github-actions bot commented Nov 24, 2023 •

edited

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