CLI Reference

Command-line reference for all bactopia-py CLI commands (v2.1.2).

User & Developer Commands

Commands for preparing inputs, querying databases, and developing Bactopia components.

Command	Description
bactopia-atb-downloader	Download All-the-Bacteria assemblies based on input query
bactopia-atb-formatter	Restructure All-the-Bacteria assemblies to allow usage with Bactopia Tools
bactopia-catalog	Generate machine-readable catalog of all Bactopia components.
bactopia-citations	Print or validate citations used throughout Bactopia.
bactopia-datasets	Download optional datasets to supplement your analyses with Bactopia
bactopia-docs	Validate reference-doc staleness across a Bactopia repo.
bactopia-download	Builds Bactopia environments for use with Nextflow.
bactopia-lint	Lint Bactopia pipeline components against style guidelines.
bactopia-merge-schemas	Builds a Nextflow Schema and/or Nextflow config for a given workflow.
bactopia-prepare	Create a 'file of filenames' (FOFN) of samples to be processed by Bactopia
bactopia-prune	Removes stale Bactopia environments that no longer match current module versions.
bactopia-pubmlst-build	Build PubMLST databases for use with the 'mlst' Bactopia Tool.
bactopia-pubmlst-setup	One-time setup for interacting with the PubMLST API
bactopia-review-tests	Review nf-test results with grouped error analysis and timing checks.
bactopia-scaffold	Scaffold Bactopia components from bioconda/conda-forge packages.
bactopia-search	Query against ENA and SRA for public accessions to process with Bactopia
bactopia-status	Show a snapshot of the Bactopia project state.
bactopia-summary	Generate a summary table from the Bactopia results.
bactopia-sysinfo	Auto-detect host RAM and CPUs, emit Nextflow CLI fragments for local profiles.
bactopia-test	Run nf-test suites for Bactopia components.
bactopia-update	Check if modules used by Bactopia Tools have newer versions available
bactopia-workflows	Output the path to a Bactopia workflow main.nf file.

Pipeline Utility Scripts

Internal scripts called by Nextflow modules during pipeline execution.

Command	Description
bactopia-bracken-to-excel	Write Bracken abundances to an Excel file.
bactopia-check-assembly-accession	Verify NCBI Assembly accession is latest and still available.
bactopia-check-fastqs	Verify input FASTQs meet minimum requirements.
bactopia-cleanup-coverage	Reduce redundancy in per-base coverage from genomeCoverageBed output.
bactopia-kraken-bracken-summary	Update the Bracken abundances with unclassified counts.
bactopia-mask-consensus	Snippy consensus (subs) with coverage masking.
bactopia-scrubber-summary	Create a before-and-after report from human read scrubbing.
bactopia-teton-prepare	Prepare sample sheets for downstream analysis in the Teton workflow.