tbprofiler_profile

Tags: tuberculosis mycobacterium drug-resistance amr typing variant-calling sample-scope

Detect resistance and lineages of Mycobacterium tuberculosis genomes.

Uses TBProfiler to profile Mycobacterium tuberculosis data for drug resistance and lineage information by aligning reads to a reference genome and identifying specific variants.

Uses explicit positional record fields for reads:

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

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio)

Outputs

record (
    meta: Record,
    csv: Path?,
    json: Path,
    txt: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
csv	Path?	Results in CSV format
json	Path	Compressed JSON results file
txt	Path?	Results in text format
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

TB-Profiler Profile Parameters

Parameter	Type	Default	Description
--tbprofiler_call_whole_genome	boolean	false	Call whole genome
--tbprofiler_mapper	string	bwa	Mapping tool to use. If you are using nanopore data it will default to minimap2 (choices: bwa, minimap2, bowtie2, bwa-mem2)
--tbprofiler_caller	string	freebayes	Variant calling tool to use (choices: bcftools, gatk, freebayes)
--tbprofiler_opts	string		Extra options in quotes for TBProfiler

Used By

Subworkflows

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

Workflows

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

Citations

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

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• TBProfiler
  Phelan JE, O'Sullivan DM, Machado D, Ramos J, Oppong YEA, Campino S, O'Grady J, McNerney R, Hibberd ML, Viveiros M, Huggett JF, Clark TG Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. Genome Med 11, 41 (2019)

• freebayes
  Garrison E, Marth G Haplotype-based variant detection from short-read sequencing. arXiv preprint arXiv:1207.3907 [q-bio.GN] (2012)

Source

View source on GitHub

Version

TBPROFILER_PROFILE:
    - tb-profiler: 6.7.0