Command Line

BfxPM uses the Typer library to provide a rich CLI experience. The syntax is universally:

bfxpm [COMMAND] [OPTIONS] or

bfxpm [GROUP] [COMMAND] [OPTIONS]

Main Commands

Command	Description
bfxpm init	Initializes a new project. Prompts for author name and GitHub username. If Git is enabled, it asks for your ORCID ID and scaffolds Open Source governance files (LICENSE, CITATION.cff, etc.) with your specific attribution.
bfxpm map	Creates a JSON map of the current directory structure. Use --rollback or -r with a path to a map file to revert your files back to the structure recorded in that snapshot.
bfxpm organize	Automatically routes scattered files (like .fastq to data/raw_external/ or .py to scripts/) and intelligently prompts you on unknown directories.
bfxpm projects	Scans a root directory for all BfxPM projects. Displays a table with names, authors, dates, and file counts. Use --html to generate a standalone web index of your research portfolio.
bfxpm tree	Outputs a visual, rich-text tree view of the current project directory. Use --all or -a to show hidden files (e.g. .git).
bfxpm report	Generates HTML/Markdown summary reports containing git history metrics, file usage stats, directory layouts, and dumps out accompanying summary.json and summary.yml metadata files.
bfxpm save	A wrapper to git commit -a -m "BfxPM Autosave" to easily snapshot current scripts and configs.
bfxpm history	Views a beautiful timeline of script modifications based on your Git history.
bfxpm sync	Syncs code (Git) and optionally data (Rsync). Use --data and --remote [PATH] for large data transfers.
bfxpm modify	Manually prompts you to safely move any arbitrary files or directories to a new project location.
bfxpm scan	Scans a directory for files, summarizing extensions and estimating disk usage.
bfxpm run_history	Scrapes your ~/.bash_history and ~/.zsh_history to extract complex executed bioinformatics commands and formats them for reproducibility.
bfxpm show	Shows all the hidden files (like .json internal caches) in the project folder.
bfxpm ai	Access the Agentic AI BioAssistant for project management and research help.
bfxpm exit	Safely terminate the BfxPM session with a status summary. Type q, exit, or abort at any prompt to cancel the setup process immediately.

Options

$ bfxpm tree --help 

Usage: bfxpm tree [OPTIONS] [PATH]                                                                          
Show a beautiful tree view of the directory and files.                                                                                                                              
╭─ Arguments ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│   path      [PATH]  Directory to show tree for [default: .]                                                                          │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --pager      --no-pager      Use a pager for the output [default: pager]                                                             │
│ --all    -a                  Show hidden files and directories                                                                       │
│ --icons                      Show emojis/icons                                                                                       │
│ --help                       Show this message and exit.                                                                             │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Sub-Command Groups

BfxPM bundles specific domain functions into logical groups.

bfxpm clean

Manage and clean project disk space.

Sub-command	Argument / Option	Description
temp	None	Automatically scans for .sam and .tmp files. Prompts before permanently deleting them.
compress	--mode	Lossless compression. standard (tar.gz), genomic (CRAM/POD5), or best (automatic).
decompress	--keep	Restores archives (.tar.gz, .gz) and specialized formats (CRAM to BAM, POD5 to FAST5).
archive	[FOLDER_NAME]	Moves an outdated or completed folder safely into an archive/ internal silo to keep the root directory neat.

bfxpm env

Manage standard bioinformatics environments.

Sub-command	Argument / Option	Description
init	None	Creates a boilerplate environment.yml for Conda / Micromamba environments.
docker	None	Creates a basic Dockerfile configured to ingest environment.yml.
singularity	None	Creates a Singularity.def (Apptainer) optimized for HPC workload encapsulations.

bfxpm pipeline

Scaffold analysis pipelines.

Sub-command	Argument / Option	Description
snakemake	None	Drops a minimal, fully configured Snakefile template in scripts/snakemake/.
nextflow	None	Drops a main.nf and nextflow.config scaffold into scripts/nextflow/.

bfxpm fetch

Fetch and route external biological data directly to designated endpoints.

Sub-command	Argument / Option	Description
sra	[SRR_ID]	Leverages fastq-dump to download dataset splits directly into data/raw_external/.
ensembl	[BUILD]	(Placeholder) Wraps curl/wget to pull reference FASTA strings to data/references/.

bfxpm checksum

Manage data integrity using MD5 checksums.

Sub-command	Argument / Option	Description
generate	None	Scans data/ and creates a checksums.md5 manifest.
verify	None	Verifies files against the manifest to detect corruption.

bfxpm flow

Record interactive terminal sessions into reproducible scripts.

Sub-command	Argument / Option	Description
start	None	Begins monitoring shell history for new commands.
stop	[NAME]	Filters history and saves commands to a .sh script in scripts/.

bfxpm deposit

Prepare and deposit project data to public repositories.

Sub-command	Argument / Option	Description
list	None	Lists all supported public data repositories (Zenodo, FigShare, Dryad, etc.) with their URLs.
prepare	--output, --include-data, --include-results	Creates a clean ZIP bundle of the project for deposition, excluding .git, .venv, and temporary files.
go	[REPO_NAME]	Opens the deposit page for the chosen repository (e.g., zenodo, figshare) directly in your browser.

bfxpm ai

Agentic AI for bioinformatics project management.

Sub-command	Argument / Option	Description
setup	None	Interactive setup for AI providers (Gemini, Ollama), models, and API keys.
ask	[QUERY]	Send a single question to the BioAssistant and get an immediate response.
chat	None	Enter an interactive, project-aware chat session with the BioAssistant.