Dev -> master for 3.14.0 release #1156

drpatelh · 2024-01-05T10:25:12Z

No description provided.

Bump versions for work on 3.14.0 milestone

Update action tower launch to v2

Update FastQC and UMItools modules

MultiQC dupRadar custom plot: specify plot_type explicitly

fix to #1150: reinstate conditional

Bump container versions for tools using Docker V1 manifest

Co-authored-by: Harshil Patel <[email protected]>

Prerelease 3.14.0 fixes

github-actions · 2024-01-05T10:28:50Z

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

Posted for pipeline commit eb5392a

+| ✅ 145 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
nextflow_config - Config manifest.version should end in dev: 3.14.0
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
pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
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-rnaseq_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-rnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-rnaseq_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: lib/WorkflowRnaseq.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-rnaseq_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
nextflow_config - nextflow.config contains configuration profile test
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/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-rnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_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
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
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 (273 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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: cloud_tests_full.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 2.11.1
Run at 2024-01-08 15:23:37

… issue

Add slash to outdir for cloud tests to fix Azure validation…

pinin4fjords

LGTM (unsurprisingly since I did a fair chunk of it).

Approval from a less biased reviewer would still be much appreciated.

adamrtalbot

Looks pretty straightforward.

Bump MultiQC version from 1.17 -> 1.19

maxulysse

LGTM

Final prerelease fixes to fix Cloud CI

pinin4fjords and others added 30 commits November 21, 2023 11:44

Bump versions for work on 3.14.0 milestone

9eadd68

[automated] Fix linting with Prettier

e9ebeaa

Merge pull request #1129 from nf-core/bump_release_dev

700664f

Bump versions for work on 3.14.0 milestone

Update cloud_tests_full to action-tower-launch-v2

0156233

Update cloud_tests_small to action-tower-launch v2

5371d63

Make output directory path instead of file?

0a1d53a

Run on self-hosted

73fd071

Revert self-hosted

d66151d

Add revision parameter to action

c958a01

Update CHANGELOG.md

dbb185f

Add PR to CHANGELOG

a9f5810

MultiQC dupradar custom plot: specify plot_type explicitly

dc2d75e

Update FastQC and UMItools modules

277af7d

Update CHANGELOG

d6803dc

Merge pull request #1135 from nf-core/update-action-tower-launch-to-v2

f92aa38

Update action tower launch to v2

Merge branch 'dev' into dev

8fed9ff

Update modules with stderr updated

8e66ae3

Update Changelog

c9fd01c

Fix formatting

9e5cdc7

Update channel names from bam_rseqc subworkflow update

75dde11

Update bam_rseqc subworkflow again

a294bb5

Update CHANGELOG.md

ed2b8aa

Merge pull request #1138 from mahesh-panchal/dev

f55a154

Update FastQC and UMItools modules

Merge pull request #1137 from vladsavelyev/multiqc-dupradar-plottype

e4c8d67

MultiQC dupRadar custom plot: specify plot_type explicitly

Template update for nf-core/tools version 2.11

efff19f

Template update for nf-core/tools version 2.11.1

0ad0970

Try more flexible requires for genome

d445520

Prettier

db3702d

Provide interface to pseudoaligner kmer length

8de95b7

Update CHANGELOG

aeab5ff

pinin4fjords and others added 15 commits January 4, 2024 09:46

Update CHANGELOG.md

456b11b

Merge pull request #1151 from nf-core/fix_gtf_flexibility

cd3a4f5

fix to #1150: reinstate conditional

Bump qualimap version to 2.3

5017588

Bump rseqc version to 5.0.3

709b7ba

[skip ci] Patch qualimap and rseqc modules

6edb3c1

Update CHANGELOG

5b0a148

Merge pull request #1152 from drpatelh/fixes

63df1d7

Bump container versions for tools using Docker V1 manifest

Disable additional multiqc versions section

cc63dff

Defer strand inference until after trimming and filtering

e86ea02

[skip ci] bump versions

282e972

Fix conditional publishing to avoid empty dirs

213d904

[skip ci] update changelog

7843299

Merge branch 'dev' into prerelease_3.14.0_fixes

fbb50ce

Apply suggestions from code review

f06f298

Co-authored-by: Harshil Patel <[email protected]>

Merge pull request #1154 from nf-core/prerelease_3.14.0_fixes

7ab1724

Prerelease 3.14.0 fixes

drpatelh and others added 3 commits January 5, 2024 10:36

[skip ci] Add slash to outdir for cloud tests to fix Azure validation…

0fb6002

… issue

Update CHANGELOG

5899b4c

Merge pull request #1157 from drpatelh/fixes

0e79758

Add slash to outdir for cloud tests to fix Azure validation…

pinin4fjords approved these changes Jan 5, 2024

View reviewed changes

adamrtalbot approved these changes Jan 5, 2024

View reviewed changes

drpatelh and others added 5 commits January 7, 2024 10:12

Bump MultiQC version from 1.17 -> 1.19

665ea7d

[skip ci] Bump CHANGELOG

0d859f7

Update CHANGELOG

aa1e043

Fix prettier

46eaf78

Merge pull request #1159 from drpatelh/fixes

805c5ac

Bump MultiQC version from 1.17 -> 1.19

maxulysse approved these changes Jan 8, 2024

View reviewed changes

drpatelh and others added 2 commits January 8, 2024 15:01

Final prerelease fixes

36c89c1

Merge pull request #1160 from drpatelh/fixes

eb5392a

Final prerelease fixes to fix Cloud CI

drpatelh merged commit b89fac3 into master Jan 8, 2024
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Dev -> master for 3.14.0 release #1156

Dev -> master for 3.14.0 release #1156

drpatelh commented Jan 5, 2024

github-actions bot commented Jan 5, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

pinin4fjords left a comment

adamrtalbot left a comment

maxulysse left a comment

Dev -> master for 3.14.0 release #1156

Dev -> master for 3.14.0 release #1156

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drpatelh commented Jan 5, 2024

github-actions bot commented Jan 5, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

pinin4fjords left a comment

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github-actions bot commented Jan 5, 2024 •

edited

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