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Published 20 hours ago • verified publisher icon nf-core

Allow multiple bracken profiles with different `-l` levels from the same kraken2 report

Open MajoroMask opened this issue 1 year ago • 1 comments

Description of feature

Bracken allows user to get report on certain taxonomy level from a single kraken2 report via bracken -l LEVEL option. Introducing this feature into TaxProfiler can be useful.

TODO

  • New parameter bracken_level: a string of bracken supported level(s) separated by comma, eg: 'G,S,S1'
    • Params checking in lib/WorkflowTaxprofiler.groovy
  • Implant feature needs:
    • subworkflows/local/profiling.nf: ch_input_for_bracken to combine() level info then add to meta.bracken_level
    • subworkflows/local/standardisation_profiles.nf: ch_profiles_for_bracken to groupTuple() on different meta.bracken_level
  • Change params using and publishDir accordingly in conf/modules.config

MajoroMask avatar Oct 27 '23 01:10 MajoroMask

It seems it has to be on hold until these two got fixed:

  • https://github.com/nf-core/modules/issues/4246
  • https://github.com/taxprofiler/taxpasta/issues/73

MajoroMask avatar Oct 27 '23 03:10 MajoroMask