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