Dev to main by DLBPointon · Pull Request #47 · sanger-tol/curationpretext

DLBPointon · 2024-12-10T08:09:02Z

Dev to Main

Dp24 spelling

github-actions · 2024-12-10T08:10:28Z

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

Posted for pipeline commit bfdaaf0

+| ✅ 123 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ 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: '1.1.0'
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in base.config: Check the defaults for all processes
schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_light.png
files_exist - File is ignored: docs/images/nf-core-curationpretext_logo_dark.png
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/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-curationpretext_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
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/curationpretext/curationpretext/.github/workflows/awstest.yml
multiqc_config - 'assets/multiqc_config.yml' not found

✅ 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: 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: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: lib/WorkflowCurationpretext.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-curationpretext_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/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html 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 (252 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: sanger_test_full.yml
actions_schema_validation - Workflow validation passed: sanger_test.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.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
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.8
Run at 2024-12-13 17:21:27

Main Backmerge into Dev

DLBPointon · 2024-12-12T12:02:30Z

The above changes you've requested are in #49

@muffato

Updates suggested by @muffato

muffato · 2024-12-13T14:21:01Z

In terms of code, this seems to be simply #48 and #49 , which have been reviewed. All tests pass ✔️

I've spotted several things through my checks:

The 1.0.1 tag is on the dev branch (c7f75f9) rather than main (fee2c39, make a new release #40). Since it's already been pushed, let's leave it as it is.
Actually, the 1.0.1 changelog is missing. Can you add it ?
The Zenodo integration has never run, but there's a DOI: https://doi.org/10.5281/zenodo.12773958 . Did you upload manually to Zenodo ?
The DOI needs to be added to README.md, nextflow.config, CITATION.cff
Update the version and check the authorship in CITATION.cff
docs/usage.md and docs/output.md haven't changed. From the code, it indeed looks like nothing changed in terms of input/output. Can you confirm ?

DLBPointon · 2024-12-13T16:13:24Z

Thanks for the review, Matthieu.

The tag must have accidentally been on dev.

I've added the 1.0.1 changelog, there wasn't much, and updated the DOI in the above files.

There hasn't been any change to the fundamentals of the pipeline in terms of operation or flags.

Zenodo was updated manually.

muffato · 2024-12-13T17:10:43Z

Zenodo was updated manually.

Ah. The GitHub integration will create another DOI because it doesn't know it needs to reuse the existing one.
Let me contact the Zenodo helpdesk see if we can force that. Otherwise we'll have to update the DOI again post release

muffato · 2024-12-13T17:19:49Z

Hum, wait a sec. This is what I can see on the Zenodo interface:

which suggests that the existing uploads are recognised.

Let's just merge this in. In the worst case we'll change the DOI in the next release but even if that happens, existing links will still work

Citations and Changelog

DLBPointon and others added 22 commits December 5, 2024 13:43

Updating

111aa60

Updating modules

080321e

Updating version to 1.1

84817a6

Merge branch 'dev' into dp24_spelling

28415b4

Updating more

4d72e53

prettier linting

d406a12

Updating setup from 1 to 2

058ed13

Adding tuple declaration

1e0f35e

Replace generate_csv singularity container

69fe17d

Updating testing

8805be5

Replace 0.0.2-yy5-c3 with 0.0.3-yy5-c1

147b88f

Remove anaconda ref in Utils and CITATIONS

0eb48b6

PRETTIER

4a1b70f

Changing grep to actually get the version info

84b1bce

Removing params

ff74ae3

Changing version command, confirmed locally and in container

2764466

Changin PERL version string and Updating executor values

3c15e2d

Readding defaults

9ad902d

ONE SPACE caused version to not print

c6a2199

Correct versioning information in modules

55756f1

Updating the changelog

3d75460

Merge pull request #45 from sanger-tol/dp24_spelling

3100655

Dp24 spelling

DLBPointon added documentation Improvements or additions to documentation enhancement New feature or request 1.1.0 addition labels Dec 10, 2024

DLBPointon requested review from muffato and weaglesBio December 10, 2024 08:09

DLBPointon self-assigned this Dec 10, 2024

Merge branch 'main' into dev

b9b9b8e

DLBPointon and others added 4 commits December 12, 2024 11:14

Updating the CICD

5c7997e

Merge pull request #48 from sanger-tol/dev_main_update

5611a0d

Main Backmerge into Dev

Updates suggested by @muffato

f7e8627

Merge branch 'dev' into dev_main_update

88aea92

DLBPointon requested a review from muffato December 12, 2024 12:02

Merge pull request #49 from sanger-tol/dev_main_update

faa038e

Updates suggested by @muffato

Citations and Changelog

50c05e1

DLBPointon and others added 2 commits December 13, 2024 16:14

Merge branch 'dev' into dev_main_update

1a45eaa

Prettier linting

6151b22

Merge pull request #50 from sanger-tol/dev_main_update

bfdaaf0

Citations and Changelog

muffato approved these changes Dec 13, 2024

View reviewed changes

DLBPointon merged commit 1359a9e into main Jan 9, 2025

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Dev to main#47

Dev to main#47
DLBPointon merged 32 commits intomainfrom
dev

DLBPointon commented Dec 10, 2024

Uh oh!

github-actions bot commented Dec 10, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

DLBPointon commented Dec 12, 2024

Uh oh!

muffato commented Dec 13, 2024

Uh oh!

DLBPointon commented Dec 13, 2024

Uh oh!

muffato commented Dec 13, 2024

Uh oh!

muffato commented Dec 13, 2024

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

DLBPointon commented Dec 10, 2024

Uh oh!

github-actions bot commented Dec 10, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

DLBPointon commented Dec 12, 2024

Uh oh!

muffato commented Dec 13, 2024

Uh oh!

DLBPointon commented Dec 13, 2024

Uh oh!

muffato commented Dec 13, 2024

Uh oh!

muffato commented Dec 13, 2024

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

github-actions bot commented Dec 10, 2024 •

edited

Loading

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