basic pipeline

This workflow will run on fastq and/or fasta (depending user supplied input) and is the first step in all other workflows implmented by bohra. It can also be used alone as a simply quality control workflow.

flowchart LR
sequence --> sequence_assessment --> report
sequence --> speciation --> report

bohra run basic -i input_file.tsv -j my_basic_pipeline

where - -i/--input_file is a tab-delimited file formatted as described here - -j/--job_id is the name of your run. This value will appear on your report.