Mycobacterium tuberculosis workflow

[ryanjameskennedy]

A new subworkflow for TB is required ASAP. The following is required for full implementation:

• TBProfiler
• [ ] Create a module that fetches variants of interest from FoHM (xlsx -> csv) and WHO (csv hopefully)
• [ ] Documentation on how to update tool database
• [ ] Prp incorporation of json output
• [ ] Add singularity image for tb-profiler:4.4.2--pyh7cba7a3_0
• [ ] Check how to manually add to tbdb
• Mykrobe
• [ ] Prp incorporation of json or csv output
• [ ] Add singularity image for mykrobe:0.12.2--py39h70e0db4_0
• Snippy
• [ ] Main module: maps and uses freebayes for variants
• [ ] Documentation on other submodule that gets core snps and how to run IQ-TREE to create phylogenetic tree (cannot be run in workflow)
• [ ] Add singularity image for snippy:4.6.0--hdfd78af_2

Note: cgMLST is not pertinent regarding epityping but can still be implemented out of interest

[ryanjameskennedy]

The incorporation of TB will require us to create workflows and subworkflows in order to separate certain modules from being run when they're not needed. I was thinking of separating the current workflow into the following groups:

• assembly
• clean?
• epityping
• processing
• quality_control
• screening

How does that sound @LordRust?