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LAST alignment statistics for MultiQC

Open charles-plessy opened this issue 1 year ago • 0 comments

This PR adds a multiqc output channel to the last/train, last/lastal and last/split modules. The new channel provides statistics in TSV format.

For last/lastal the MultiQC file contains some of the alignment parameters determined by this module. Their value is quickly retrieved by parsing a text file.

For last/lastal and last/split, the MultiQC file contains the total alignment length and percent similarity computed on the fly while the alignment is being performed.

PR checklist

  • [x] This comment contains a description of changes (with reason).
  • [x] 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
  • [x] If necessary, include test data in your PR.
  • [x] Remove all TODO statements.
  • [x] Emit the versions.yml file.
  • [x] Follow the naming conventions.
  • [x] Follow the parameters requirements.
  • [x] Follow the input/output options guidelines.
  • [x] Add a resource label
  • [x] 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:
      • [x] nf-core modules test <MODULE> --profile docker
      • [x] nf-core modules test <MODULE> --profile singularity
      • [x] 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

charles-plessy avatar Jul 02 '24 08:07 charles-plessy