Assemblyscan 1.0.0

[eit-maxlcummins]

Description

This updates the assemblyscan module to v1.0.0 from v0.4.0, enabling tsv or json output.

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 module conventions in the contribution docs
• [-] If necessary, include test data in your PR.
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• Emit the versions.yml file.
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[prototaxites]

@nf-core-bot fix linting

[prototaxites]

This looks really good, but can we add a second test to validate JSON output?

[SPPearce]

Just to check, was this previously producing a tsv output but calling it a .json file? ☹️

It'd be nice if you could swap to using a topic channel to capture the version too: https://nf-co.re/blog/2025/version_topics

[charles-plessy]

Hi all, I am jumping in as I want to update this module in https://github.com/nf-core/pairgenomealign. assenbly-scan used to default to JSON but now changed to TSV, which is why the format changed in the test snapshot in this PR. I have prepared 3 commits that:

• add tests for JSON output,
• switch to version topic channel, and
• add a stub.
  I thought I could push them to the PR but failed and created a new branch instead (master...pr-9506). Please let me know your thoughts.

[eit-maxlcummins]

@charles-plessy - thanks for your contributions. I have cherry picked your commits and added them to this PR and added you to the authorship in the meta :)

[eit-maxlcummins]

Just to check, was this previously producing a tsv output but calling it a .json file? ☹️

It'd be nice if you could swap to using a topic channel to capture the version too: https://nf-co.re/blog/2025/version_topics

Done :)

[SPPearce]

Do we just want to capture the output in one channel, rather than two separate ones? That would be within guidelines: https://nf-co.re/docs/guidelines/components/modules#one-output-channel-per-output-file-type

[dwells-eit]

Looks good 😎

[charles-plessy]

@nf-core-bot fix linting

Regarding the lint failures, I have not managed to get the tests pass with topic channels when the evaluated shell command has a $ sign in. But in the case of assemblyscan, we do not need one: eval("assembly-scan --version | sed 's/assembly-scan //'") works well enough, and then the meta.yml files can contain - "assembly-scan --version | sed 's/assembly-scan //'": without triggering errors.

[eit-maxlcummins]

@nf-core-bot fix linting

Regarding the lint failures, I have not managed to get the tests pass with topic channels when the evaluated shell command has a $ sign in. But in the case of assemblyscan, we do not need one: eval("assembly-scan --version | sed 's/assembly-scan //'") works well enough, and then the meta.yml files can contain - "assembly-scan --version | sed 's/assembly-scan //'": without triggering errors.

@charles-plessy Thanks! Was playing around with that exact issue right now. Passes locally but the GitHub runner runs a dev version of nf-core tools.

Will trim the regex to remove $ if it fails now. Thanks for sharing :)