PR for 2.2.4 bugfix release #296

apeltzer · 2023-11-03T15:50:08Z

PR checklist

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

Bugfix release 2.2.4 for mirtop gff issues

Bump Module Versions to latest versions (includes MQC 1.17)

github-actions · 2023-11-03T15:52:30Z

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

Posted for pipeline commit 5a307a6

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

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.2.4
pipeline_todos - TODO string in WorkflowSmrnaseq.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-smrnaseq_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-smrnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-smrnaseq_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/WorkflowSmrnaseq.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-smrnaseq_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-smrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-smrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-smrnaseq_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 (159 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 2023-11-03 19:30:20

maxulysse · 2023-11-03T15:55:43Z

modules/nf-core/custom/dumpsoftwareversions/environment.yml

+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::multiqc=1.15


there's a newer version of this module

maxulysse · 2023-11-03T15:57:30Z

no multiqc update?

FriederikeHanssen

lgtm

nextflow.config

apeltzer · 2023-11-03T17:22:58Z

no multiqc update?

modules/nf-core/multiqc/environment.yml ? 😉

nf-core-bot and others added 30 commits June 30, 2023 16:15

Template update for nf-core/tools version 2.9

d0d600a

Also clean up GFF

c8e2250

Push fix

25adf79

Bump version and changelog

c6c3ff9

Prettier

0ab71ae

More sed magic

0d6aeef

Proper exiting of variables in sed expression ...

d33232d

Hopefully fix

ce3894a

Remove trailing newlines in FastA too

53c0608

Cleaned up

263fb62

Fix for mirTop

c65dc16

Add suggestions by @mdozmorov

21b10e9

Template update for nf-core/tools version 2.10

1c25684

fix input for mirdeep2 run

963b02e

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

4f5a4e1

fix container error

bb5f1e3

recover module version

1dc608f

attempt to fix prettier error

df0a002

Merge pull request #290 from nf-core/nf-core-template-merge-2.10

1aeb518

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

Merge branch 'dev' into fix-mirtop-gff

0113f55

fix some lint warnings

b2b3d99

Hopefully fixing last lint error

256da50

Missing dev statement towards dev branch

4c27e8c

Merge pull request #281 from nf-core/fix-mirtop-gff

ed3d869

Bugfix release 2.2.4 for mirtop gff issues

Update other modules

14d72a9

Changelog

2e3ec8a

Merge pull request #293 from nf-core/bump-mqc

12b09d3

Bump Module Versions to latest versions (includes MQC 1.17)

PR for 2.2.4 release

f0df016

Add proper changelog

442ce1b

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

3c9bf88

Remove stuff we didnt want in

892fc85

maxulysse reviewed Nov 3, 2023

View reviewed changes

FriederikeHanssen approved these changes Nov 3, 2023

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maxulysse approved these changes Nov 3, 2023

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Add doi

5a307a6

apeltzer merged commit 87f2b3e into master Nov 3, 2023
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PR for 2.2.4 bugfix release #296

PR for 2.2.4 bugfix release #296

apeltzer commented Nov 3, 2023

github-actions bot commented Nov 3, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

maxulysse Nov 3, 2023

maxulysse commented Nov 3, 2023

FriederikeHanssen left a comment

apeltzer commented Nov 3, 2023

PR for 2.2.4 bugfix release #296

PR for 2.2.4 bugfix release #296

Conversation

apeltzer commented Nov 3, 2023

PR checklist

github-actions bot commented Nov 3, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

maxulysse Nov 3, 2023

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maxulysse commented Nov 3, 2023

FriederikeHanssen left a comment

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apeltzer commented Nov 3, 2023

github-actions bot commented Nov 3, 2023 •

edited

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