Release 0.10.0 #38

ksenia-krasheninnikova · 2024-04-15T09:53:52Z

New release for organelles subworkflow

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2024-04-15T09:56:10Z

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

Posted for pipeline commit eb3f9a6

+| ✅ 129 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
nextflow_config - Config manifest.version should end in dev: '0.9.1'
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-genomeassembly_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_light.png
files_exist - File is ignored: docs/images/nf-core-genomeassembly_logo_dark.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
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
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-genomeassembly_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-genomeassembly_logo_dark.png
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/genomeassembly/genomeassembly/.github/workflows/awstest.yml

✅ 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/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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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/NfcoreSchema.groovy
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: lib/WorkflowGenomeassembly.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: .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-genomeassembly_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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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.show_hidden_params
nextflow_config - Config variable found: params.schema_ignore_params
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 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 - .github/.dockstore.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 - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreSchema.groovy 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: 22.10.1, Config: 22.10.1
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 (233 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/yaml'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.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 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2024-04-16 14:21:26

ksenia-krasheninnikova · 2024-04-15T14:15:19Z

@gq1 PR is ready for review. Many thanks.

CHANGELOG.md

gq1 · 2024-04-15T15:57:36Z

CHANGELOG.md

-### `Deprecated`
-
-## [[0.9.0](https://github.com/sanger-tol/genomeassembly/releases/tag/0.9.0)] - Night Fury - [2023-12-15]
+## [[0.9.1](https://github.com/sanger-tol/genomeassembly/releases/tag/0.9.1)] - Hideous Zippleback - [2024-04-15]

 Initial release of sanger-tol/genomeassembly, created with the [nf-core](https://nf-co.re/) template.


And then this line can be removed for release 0.9.1 changes.

gq1 · 2024-04-15T16:00:24Z

Here is the updated version of release instruction from @muffato.
https://pipelines.tol.sanger.ac.uk/docs/contributing/pipeline-release
It seems you did a lots of changes for this release, probably not a small number change, but you already on 0.9. Probably it will be ok.

muffato · 2024-04-15T20:01:57Z

I agree. 0.9.1 would be for bug-fixes only. Here you've got real features and differences. This should be 0.10.0

Updates based on code review

Add description about plastid

ksenia-krasheninnikova · 2024-04-16T12:24:22Z

Addressed the comments from the code review.
Also, updated the code in order to be able to optionally switch on plastid search in oatk - this was missed in the previous PR.
And updated the json schema for the input yaml file.
I will only need to update the release date if there are no other comments.
Ready for re-review @gq1 @muffato

CHANGELOG.md

Bump new version

fd44496

ksenia-krasheninnikova and others added 3 commits April 15, 2024 11:55

Update CHANGELOG.md

0eaff6c

Dump software versions out of for ORGANELLES subworkflow

0712e8b

Prettier fix

a847428

ksenia-krasheninnikova requested a review from gq1 April 15, 2024 12:01

ksenia-krasheninnikova and others added 5 commits April 15, 2024 13:04

Update README.md

340a10f

Updated organelles image

83a4637

Update output.md

2264b87

Rename the image file

d5cd163

Make sure oatk output is published

1b96c57

gq1 reviewed Apr 15, 2024

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gq1 reviewed Apr 15, 2024

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Ksenia Krasheninnikova and others added 2 commits April 16, 2024 10:47

Add support for plastid for oatk (optional)

85310d1

Update CHANGELOG.md

0d55f15

Updates based on code review

ksenia-krasheninnikova changed the title ~~Release 0.9.1~~ Release 0.10.0 Apr 16, 2024

ksenia-krasheninnikova and others added 2 commits April 16, 2024 10:58

Update output.md

3dec51b

Add description about plastid

Update schema description

838914f

ksenia-krasheninnikova requested a review from gq1 April 16, 2024 12:24

gq1 reviewed Apr 16, 2024

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ksenia-krasheninnikova requested a review from gq1 April 16, 2024 14:10

gq1 approved these changes Apr 16, 2024

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Update release date

eb3f9a6

ksenia-krasheninnikova merged commit 0276f81 into dev Apr 16, 2024
6 checks passed

muffato deleted the release-0.9.1 branch May 29, 2024 07:54

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Release 0.10.0 #38

Release 0.10.0 #38

ksenia-krasheninnikova commented Apr 15, 2024

github-actions bot commented Apr 15, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ksenia-krasheninnikova commented Apr 15, 2024

gq1 Apr 15, 2024

gq1 commented Apr 15, 2024

muffato commented Apr 15, 2024

ksenia-krasheninnikova commented Apr 16, 2024 •

edited

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Release 0.10.0 #38

Release 0.10.0 #38

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ksenia-krasheninnikova commented Apr 15, 2024

PR checklist

github-actions bot commented Apr 15, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

ksenia-krasheninnikova commented Apr 15, 2024

gq1 Apr 15, 2024

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gq1 commented Apr 15, 2024

muffato commented Apr 15, 2024

ksenia-krasheninnikova commented Apr 16, 2024 • edited Loading

github-actions bot commented Apr 15, 2024 •

edited

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

ksenia-krasheninnikova commented Apr 16, 2024 •

edited

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