abricate_summary

Tags: bacteria tab-delimited antimicrobial-resistance run-scope

Summarize Abricate screening results.

Uses Abricate to aggregate the per-sample screening reports into a single tab-delimited summary file.

Inputs

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

Field	Type	Description
meta	Record	Groovy Record containing aggregation information
reports	Set<Path>	A collection of Abricate report files from multiple samples

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Aggregated tab-delimited summary of Abricate results from all samples
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

Used By

Subworkflows

• abricate - Mass screening of contigs for antimicrobial and virulence genes.

Workflows

• abricate - Mass screening of contigs for antimicrobial resistance and virulence genes.

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)

• Abricate
  Seemann T Abricate: mass screening of contigs for antimicrobial and virulence genes (GitHub)

Source

View source on GitHub

Version

ABRICATE_SUMMARY:
    - abricate: 1.4.0