Collect different peer-reviewed pipelines for MTBC

[abhi18av]

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]

List of experimental candidates:

• https://github.com/cvn001/transflow

[abhi18av]

https://github.com/abhi18av-forked-repos/lodestone