nf-core / nf-core/modules

new module (collection): CRABS

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#7,496 2 comments 0 reactions 1 assignee View on GitHub

@xHaMMaDy is already working on this.

Since Sep 13, 2026.

good first issue new module
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Description

Is there an existing module for this?
  • I have searched for the existing module
Is there an open PR for this?
  • I have searched for existing PRs
Is there an open issue for this?
  • I have searched for existing issues
Further Information

To port the existing crabs modules (insilicopcr & dbimport) from nf-core/readsimulator the crabs modules need to be extended by the new functions from v1.0.7 onwards:

https://github.com/gjeunen/reference_database_creator?tab=readme-ov-file#5-crabs-workflow

Submodules that can be implemented

Only crabs/merge are necessary for the porting. Needed to close https://github.com/nf-core/modules/pull/6583

  • crabs/merge
  • crabs/pairwiseglobalalignment
  • crabs/dereplicate
  • crabs/filter
  • crabs/subset
  • crabs/export
  • crabs/download (this takes multiple flags)

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