A tool to detect resistance and lineages of M. tuberculosis genomes
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
FASTQ file
*.{fastq.gz,fq.gz}
bam
bam/*.bam
BAM file with alignment details
*.bam
csv
results/*.csv
Optional CSV formatted result file of resistance and strain type
*.csv
json
results/*.json
JSON formatted result file of resistance and strain type
*.json
txt
results/*.txt
Optional text file of resistance and strain type
*.txt
vcf
vcf/*.vcf.gz
VCF with variant info again reference genomes
*.vcf
versions
versions.yml
File containing software versions
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
