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Add SubWorkflow: mmseqs_contig_taxonomy

Open Darcy220606 opened this issue 3 months ago • 0 comments

PR checklist

Purpose: This PR adds a subworkflow that combines multiple mmseqs tools. Function: This adds taxonomic classification to input 'nucleotide' sequences (e.g. contigs) , which can potentially be used in multiple pipelines, e.g. nf-core/funcscan and nf-core/taxprofiler.

  • [x] This comment contains a description of changes (with reason).
  • [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [x] 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.
  • [x] Remove all TODO statements.
  • [x] Emit the versions.yml file.
  • [x] Follow the naming conventions.
  • [ ] Follow the parameters requirements.
  • [x] Follow the input/output options guidelines.
  • [x] 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
    • For subworkflows:
      • [x] nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • [x] nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • [x] nf-core subworkflows test <SUBWORKFLOW> --profile conda

Darcy220606 avatar Apr 25 '24 08:04 Darcy220606