Description

A tool to detect resistance and lineages of M. tuberculosis genomes

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

FASTQ file

*.{fastq.gz,fq.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

bam (file)

BAM file with alignment details

*.bam

csv (file)

Optional CSV formated result file of resistance and strain type

*.csv

json (file)

JSON formated result file of resistance and strain type

*.json

txt (file)

Optional text file of resistance and strain type

*.txt

vcf (file)

VCF with variant info again refernce genomes

*.vcf

Tools

tbprofiler
GPL v3

Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data