Skip to content

Added new module arcane/express - #12952

Merged
LeonHornich merged 6 commits into
nf-core:masterfrom
LeonHornich:arcane_express
Sep 29, 2026
Merged

LeonHornich merged 6 commits into
nf-core:masterfrom
LeonHornich:arcane_express

Conversation

@LeonHornich

@LeonHornich LeonHornich commented Sep 14, 2026 •

Copy link
Copy Markdown
Contributor

Added new module supporting arcane/express subcommand.

Quick things to add/consider:

process {
    withName: 'ARCANE_FILTER' {
        ext.args = '--kmersize 12'
    }
    withName: 'ARCANE_INDEX' {
        ext.args = '--kmersize 12'
    }
    withName: 'ARCANE_EXPRESS' {
        ext.args = { params.express_args ?: '' }
    }
} 
  • i tried defining the --kmersize 12 parameter in the setup block directly for the /filter and /index subcommands. With that the tools /filter and /index was not able to access the parameter and did not run. Therefore these are defined directly in the config. If you have alternative options or ideas why this happens please let me know.

  • 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.

  • Remove all TODO statements.

  • Broadcast software version numbers to topic: versions - See version_topics

  • Follow the naming conventions.

  • Follow the parameters requirements.

  • Follow the input/output options guidelines.

  • Add a resource label

  • Use BioConda and BioContainers if possible to fulfil software requirements.

  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:

    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

@famosab famosab left a comment

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think this looks good :)

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think it might be related to the fact that the config needs to be supplied differently to the setup block. But I would say it is ok to leave it like that.

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

That would explain it. Is there some documentation regarding how to handle this? I haven't been able to find anything in the official docs. Just so that i know for the future :)

@LeonHornich
LeonHornich added this pull request to the merge queue Sep 29, 2026
Merged via the queue into nf-core:master with commit c99190a Sep 29, 2026
126 checks passed
@LeonHornich
LeonHornich deleted the arcane_express branch September 29, 2026 19:47
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants