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tbprofiler

Tags: mycobacterium tuberculosis drug-resistance lineage variants sample-scope

Profiling tool for Mycobacterium tuberculosis to detect resistance and strain type.

This subworkflow performs comprehensive profiling of Mycobacterium tuberculosis from sequencing reads using TBProfiler. The tool detects drug resistance mutations, determines lineage and strain type, and provides detailed variant calling results. It combines individual sample results with population-level analysis for surveillance and epidemiological studies.

Uses explicit positional record fields for reads:

  • Input: record(meta, r1, r2, se, lr) where each read slot is Path?

Take​

reads: Channel<Record>
FieldDescription
metaGroovy Record containing sample information
r1Illumina R1 reads (paired-end)
r2Illumina R2 reads (paired-end)
seSingle-end Illumina reads
lrLong reads (ONT/PacBio)

Emit​

Published​

The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.

sample_outputs​

OutputDescription
bamAligned BAM file
csvResults in CSV format
jsonCompressed JSON results file
txtResults in text format
vcfCompressed VCF file with variants

run_outputs​

OutputDescription
csvMain collated results in CSV format
variants_csvCollated variants in CSV format
variants_txtCollated variants in text format
itoliTOL formatted files for visualization

Module Composition​

This subworkflow calls the following modules:

Used By​

This subworkflow is used by the following workflows:

  • tbprofiler - Detection of antimicrobial resistance and lineage typing of Mycobacterium tuberculosis.

Citations​

If you use this in your analysis, please cite the following.

Source​

View source on GitHub