tbprofiler_collate

Tags: tuberculosis mycobacterium drug-resistance collate summary run-scope

Collate TB-Profiler results from multiple samples.

Uses TBProfiler to aggregate profiling results from multiple samples into summary tables and files suitable for phylogenetic visualization.

Inputs

record (
    meta: Record,
    json: Set<Path>
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
json	Set<Path>	List of TB-Profiler JSON output files

Outputs

record (
    meta: Record,
    csv: Path,
    variants_csv: Path,
    variants_txt: Path,
    itol: Set<Path?>,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
csv	Path	Main collated results in CSV format
variants_csv	Path	Collated variants in CSV format
variants_txt	Path	Collated variants in text format
itol	Set<Path?>	iTOL formatted files for visualization
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 Collate Parameters

Parameter	Type	Default	Description
--tbprofiler_itol	boolean	false	Generate itol config files
--tbprofiler_full	boolean	false	Output mutations in main result file
--tbprofiler_all_variants	boolean	false	Output all variants in variant matrix
--tbprofiler_mark_missing	boolean	false	An asterisk will be used to mark predictions which are affected by missing data at a drug resistance position

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)

Source

View source on GitHub

Version

TBPROFILER_COLLATE:
    - tb-profiler: 6.7.0