Release candidate 1.4.1 #177

Aratz · 2024-02-27T11:34:30Z

Solves #175

Includes the following:

`Changed`

#167 Updated template to nf-core/tools v2.12
#163 Updated template to nf-core/tools v2.11.1
#162 Updated template to nf-core/tools v2.11

Bump version to 1.5.0dev

Important! Template update for nf-core/tools v2.11

Important! Template update for nf-core/tools v2.11.1

…-2.12

Ran `nf-core modules update`

Important! Template update for nf-core/tools v2.12

Fix badges

chore: emiller88 => edmundmiller

Solves #175

This is done to solve #175 in a timely fashion. This commit should be reverted after the release is done.

Pre-release v1.4.1

github-actions · 2024-02-27T11:35:59Z

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

Posted for pipeline commit ef60565

+| ✅ 166 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.4.1
pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
pipeline_todos - TODO string in WorkflowDemultiplex.groovy: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
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 ignored:

files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
actions_ci - actions_ci

✅ 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: 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-demultiplex_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-demultiplex_logo_light.png
files_exist - File found: docs/images/nf-core-demultiplex_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/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/WorkflowDemultiplex.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-demultiplex_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: lib/nfcore_external_java_deps.jar
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.trim_fastq= true
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
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/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 - 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-demultiplex_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demultiplex_logo_light.png matches the template
files_unchanged - docs/images/nf-core-demultiplex_logo_dark.png matches the template
files_unchanged - docs/README.md 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_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 (163 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: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.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' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
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 2.12.1
Run at 2024-02-27 14:44:56

matthdsm · 2024-02-27T11:37:10Z

tests/pipeline/bases2fastq.nf.test.snap

@@ -1,9 +1,9 @@
 {
    "software_versions": {
        "content": [
-            "{BASES2FASTQ={bases2fastq=1.1.0.593880262, use subject to license available at elementbiosciences.com}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.12.0, yaml=6.0.1}, FALCO={falco=1.2.1}, FASTP={fastp=0.23.4}, UNTAR={untar=1.30}, Workflow={nf-core/demultiplex=1.4.0}}"


Why the version downgrades?

I'm not sure, this is the result of the last update of CUSTOM_DUMPSOFTWAREVERSIONS in #167 (see also nf-core/tools@93f6af8). I suspect it's linked to the MultiQC upgrade from 1.17 to 1.19, but all I could find was https://github.com/MultiQC/MultiQC/blob/19cec5cd5c967fc6a660cd7a354a11d5cff3dfbf/.github/RELEASE_CHECKLIST.md?plain=1#L29

Maybe @ewels or @mashehu know more about this.

Related, why no MultiQC 1.20?

Good question 😁 It made the tests fail in #176. For the sake of making this new release asap and because I'm a bit tight on time this week, I decided to keep it at 1.19 for now.

the downgrade of python? We ran into some errors with 3.12, so recommend 3.11 at the moment

matthdsm

One comment out of curiosity, LGTM otherwise

edmundmiller

Looks good to me! Agreed that MultiQC 1.20 can be a future release.

Aratz · 2024-02-27T14:26:46Z

Thanks! I might need some help with merging this PR, GitHub says it's out of date with the base branch, but when I click "Update branch", I get the following error message: Changes must be made through a pull request..

Probably needs help overriding the nf-core download test too 😬

CHANGELOG.md

Aratz and others added 26 commits December 15, 2023 08:44

Bump version to 1.5.0dev

9b10331

Merge pull request #161 from Aratz/dev

bddac66

Bump version to 1.5.0dev

Template update for nf-core/tools version 2.11

f5485f5

Merge branch 'dev' into nf-core-template-merge-2.11

57ac68b

Add .nf-test to .prettierignore

455dfaa

Merge pull request #162 from nf-core/nf-core-template-merge-2.11

593047f

Important! Template update for nf-core/tools v2.11

Template update for nf-core/tools version 2.11.1

0809f13

Merge pull request #163 from nf-core/nf-core-template-merge-2.11.1

45448df

Important! Template update for nf-core/tools v2.11.1

Template update for nf-core/tools version 2.12

f750781

Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…

0c27d32

…-2.12

Update all modules

6f9f7fd

Ran `nf-core modules update`

Run prettier

799245a

Update changelog

512e6a1

Fix linting

838ba72

Remove fastqc artifacts

054c08f

Update snapshots

0627d6e

Merge pull request #167 from nf-core/nf-core-template-merge-2.12

bdd466c

Important! Template update for nf-core/tools v2.12

Fix badges

d774cf1

Merge pull request #170 from Aratz/dev

c49e94d

Fix badges

chore: emiller88 => edmundmiller

e64ed20

Merge pull request #173 from nf-core/edmundmiller

de87958

chore: emiller88 => edmundmiller

Update all modules

2f02d8d

Bump version to 1.4.1

5481dda

Solves #175

Revert MultiQC update

af50ed7

Pin nf-core/tools to 2.12.1

eca503f

This is done to solve #175 in a timely fashion. This commit should be reverted after the release is done.

Merge pull request #176 from Aratz/dev

278c959

Pre-release v1.4.1

Aratz requested review from maxulysse, matthdsm, edmundmiller and nvnieuwk February 27, 2024 11:34

Aratz requested review from nh13, sam-white04, blajoie and a team as code owners February 27, 2024 11:34

matthdsm reviewed Feb 27, 2024

View reviewed changes

matthdsm approved these changes Feb 27, 2024

View reviewed changes

edmundmiller approved these changes Feb 27, 2024

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maxulysse reviewed Feb 27, 2024

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maxulysse approved these changes Feb 27, 2024

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maxulysse added 2 commits February 27, 2024 15:36

Update CHANGELOG.md

0e7d605

Merge branch 'master' into dev

ef60565

Aratz merged commit aa4d936 into master Feb 27, 2024
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Release candidate 1.4.1 #177

Release candidate 1.4.1 #177

Aratz commented Feb 27, 2024

github-actions bot commented Feb 27, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

matthdsm Feb 27, 2024

Aratz Feb 27, 2024

matthdsm Feb 27, 2024

Aratz Feb 27, 2024

mashehu Feb 27, 2024

matthdsm left a comment

edmundmiller left a comment

Aratz commented Feb 27, 2024

Release candidate 1.4.1 #177

Release candidate 1.4.1 #177

Conversation

Aratz commented Feb 27, 2024

Changed

github-actions bot commented Feb 27, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

matthdsm Feb 27, 2024

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Aratz Feb 27, 2024

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Aratz commented Feb 27, 2024

`Changed`

github-actions bot commented Feb 27, 2024 •

edited

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