amr_typing pipeline

This workflow will use user supplied species or the species detected in the sequence to determine the appropriate typing and AMR pipeline to use. Additional inferrence of genomic DST/AST will be undertaken for S. enterica and M. tuberculosis.

If assembly is required and fastq are used as input - the assembly workflow will be triggered.

Note that for AMR and gDST in M. tuberculosis paired-end fastq are required. We recommend to use the bohra run tb workflow for M. tuberculosis.

flowchart LR
fastq --> assembly --> annotation --> sequence_assessment
assembly --> typing
assembly --> AMR
assembly --> speciation
assembly --> plasmid_detection --> AMR
speciation --> typing --> report
speciation --> AMR --> report
fastq --> sequence_assessment --> report
fastq --> speciation --> report

This pipeline will use abritamr for AMR mechanism detection and undertake species appropriate serotyping (where speciation is done or species is supplied) You can provide paired-end fastq and/or assemblies as input for this pipeline. If only paired-end fastq supplied, assembly will be run to generate appropriate inputs for abritamr and serotyping. If you would like to use an assembly combination different from the default you will need to specify

where inputs are only (or mostly paired-end fastq) and you want to use a different assembler to the default of shovill + spades
```
bohra run amr_typing -i input_file.tsv -j my_typing_pipeline -a shovill_skesa --cpus X
```
where inputs are assemblies (or you are happy to stick with shovill + spades )
```
bohra run amr_typing -i input_file.tsv -j my_typing_pipeline --cpus X
```