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nf-core / tbanalyzer

An nf-core (meta) pipeline for analysis of different members of Mycobacterium tuberculosis complex.
https://nf-co.re/tbanalyzer
MIT License
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Collect different peer-reviewed pipelines for MTBC #3

Open abhi18av opened 2 weeks ago

abhi18av commented 2 weeks ago

Description of feature

The pre-requisites for the pipelines to be a part of tbanalyzer

  1. Should be published in a peer-reviewed journal

  2. Should (preferably) have some citations i.e. other projects using that pipeline

  3. Pipelines should be open-source and ideally a license which allows redistribution ( https://choosealicense.com/)

  4. Pipelines which are already in Nextflow, are initial priorities due to ease of collaboration and inclusion.

Some pipelines which fullfil this criteria

  1. MAGMA https://doi.org/10.1371/journal.pcbi.1011648

  2. MTBseq https://doi.org/10.7717/peerj.5895

  3. TBpore https://doi.org/10.1016/S2666-5247(22)00301-9

  4. Bovis pipelines (TODO)

  5. Q: TBprofiler, Mykrobe - shall we address these popular (independent) tools and allow them to be run directly?

In terms of design of each workflow/method

Style of parameters

- mtbseq-minimal-coverage: 

- magma-skip-phylogeny-and-clustering 

- tbpore-cutoff

Per-method test profiles

Add a custom test_magma , test_full_mtbseq for all methods.

Resources

  1. Github search https://github.com/topics/tuberculosis
  2. PubMed
abhi18av commented 2 weeks ago

List of experimental candidates: