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Linting for release #29

Merged
merged 16 commits into from
Jul 17, 2024
Merged

Linting for release #29

merged 16 commits into from
Jul 17, 2024

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muffato
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@muffato muffato commented Jul 16, 2024 •
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This is a PR to solve the issues flagged by nf-core lint in #28 . I've started fixing a few, but @DLBPointon can you check the other ones ?

  • when: condition has been removed
    I've added them back b9d2630
  • Found tuple but no channel names
    The parser was confused by the whitespace 68b369b
  • Module does not emit software version
    Only modules/local/reformat_intersect.nf needs fixing
  • Non-standard labels found
    process_tiny is not recognised. Switched to process_single f71aeb2
  • Specified label appears to contain non-alphanumerics and Standard process label not found
    It looks like nf-core lint didn't like the double quotes 501572c
  • 'meta' map not emitted in output channel(s)
    This is get_largest_scaff.nf
  • Config manifest.version should not contain dev for a release: and manifest.version was not numeric
    You need to bump the version number in nextflow_config and other files

I think these ones don't need fixing, but please confirm:

  • Unable to connect to container URL
    nf-core lint seems unable to parse / verify docker.io/ubuntu:20.04
  • New version available
    The versions being used have been validated in production. We don't want to change them now.
  • No template found in shell block
    That's because it expects """ ... """ but you use $/ ... /$. I guess that's on purpose to simplify the handling of $ ?
  • Container versions do not match
    I think it's complaining that the Singularity and Docker versions mismatch

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
  • If necessary, also make a PR on the sanger-tol/curationpretext branch on the nf-core/test-datasets repository.
  • 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).

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github-actions bot commented Jul 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 353325b

+| ✅ 122 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  10 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: '1.0.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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
  • 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:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-07-17 19:30:20

@muffato muffato mentioned this pull request Jul 16, 2024
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Hi @muffato

Thanks for writing this up.

  • I've now added the version output to reformat_intersect
  • For get_largest_scaff, this module outputs an env, I can't put this in a tuple can i? Would you want another channel as output to output the meta?
  • manifest.version has been corrected in the nextflow.config, where else is it changed? I see alot of files that reference manifest.version so don't need updating.

Can't be fixed

  • Yes, I see the same lint error. NF-core seems to not like the docker.io prefix. I don't think I can override that error.
  • I agree, versions should be kept the same until we can properly validate the new version.
  • Yes, i'm using $/ ... /$ here to better use bash. I'm pretty sure we used this with """...""" and awk was not having it.
  • I presume so.

@muffato
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muffato commented Jul 16, 2024

  • For get_largest_scaff, this module outputs an env, I can't put this in a tuple can i? Would you want another channel as output to output the meta?

Can you try putting the env together with meta in a tuple ? If it works, we're good. Otherwise, let's dismiss this CI test

  • manifest.version has been corrected in the nextflow.config, where else is it changed? I see alot of files that reference manifest.version so don't need updating.

Here are all the places where we have the version number: https://github.com/sanger-tol/genomenote/pull/127/files (exclude the Python script). Make sure all those files are updated in this PR here.

@muffato
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muffato commented Jul 17, 2024

Super ! I fixed the CI error, the last linting error and a few warnings. All good now

@muffato muffato self-assigned this Jul 17, 2024
@muffato muffato requested a review from DLBPointon July 17, 2024 19:54
@muffato
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muffato commented Jul 17, 2024

Up to you @DLBPointon to Approve and merge

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Up to you @DLBPointon to Approve and merge

Thanks for all the help with this @muffato !

@DLBPointon DLBPointon merged commit 6c3cf57 into dev Jul 17, 2024
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@muffato muffato deleted the release_lint branch August 16, 2024 09:22
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