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CLI Reference

This page provides a complete reference of all available SeqNado commands and options.

For quick examples and typical usage patterns, see the Quick Start Guide.

SeqNado CLI

Initialize your environment, build configs, create design files, and run pipelines. Use --help on any subcommand for details.

Usage:

$ seqnado [OPTIONS] COMMAND [ARGS]...

Options:

  • -v, --version: Show version and exit.
  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.

Commands:

  • init: Initialize SeqNado user environment.
  • genomes: Manage genome configurations (list, edit,...
  • config: Build a workflow configuration YAML for...
  • tools: List and explore bioinformatics tools...
  • download: Download FASTQ files from GEO/SRA using a...
  • design: Generate a SeqNado design CSV from FASTQ...
  • pipeline: Run the data processing pipeline for ASSAY...

seqnado init

Initialize SeqNado user environment.

  • Logs the current Conda environment if active (optional).
  • Runs packaged Apptainer/Singularity init (if apptainer on PATH).
  • Ensures ~/.config/seqnado/genome_config.json exists (template or preset).

Usage:

$ seqnado init [OPTIONS]

Options:

  • --preset / --no-preset: Use packaged preset genomes instead of the editable template. [default: no-preset]
  • --dry-run / --no-dry-run: Show actions without writing files or running scripts. [default: no-dry-run]
  • -v, --verbose: Increase logging verbosity.
  • --help: Show this message and exit.

seqnado genomes

Manage genome configurations (list, edit, build, or generate fastq-screen config)

Usage:

$ seqnado genomes [OPTIONS] SUBCOMMAND [ASSAY]

Arguments:

  • SUBCOMMAND: list, edit, build, or fastqscreen [required]
  • [ASSAY]: Assay type. Options: rna, atac, snp, chip, cat, meth, mcc, crispr, multiomics [default: atac]

Options:

  • -f, --fasta PATH: Input FASTA (required for build)
  • -n, --name TEXT: Genome name(s), comma-separated for multiple (e.g., hg38 or hg38,mm39,dm6)
  • -o, --outdir PATH: Output directory for build [default: /home/runner/work/SeqNado/SeqNado/genome_build]
  • -sp, --spikein TEXT: Spike-in genome name for composite builds (e.g., mm39)
  • --preset [lc|le|ls|ss|t]: Snakemake job profile preset (for build subcommand). [default: le]
  • -c, --cores INTEGER: Number of cores for Snakemake (for build subcommand). [default: 4]
  • --scale-resources FLOAT: Scale memory/time (for build subcommand). [default: 1.0]
  • -s, --screen PATH: Output path for fastqscreen config (fastqscreen subcommand)
  • -t, --threads INTEGER: Number of threads for Bowtie2 (fastqscreen subcommand) [default: 8]
  • --no-contaminants: Exclude contaminant databases (fastqscreen subcommand)
  • --contaminant-path PATH: Path to contaminant reference files (fastqscreen subcommand)
  • --dry-run: Pass --dry-run to Snakemake (build subcommand)
  • -v, --verbose: Increase logging verbosity
  • --help: Show this message and exit.

seqnado config

Build a workflow configuration YAML for the selected ASSAY. If no assay is provided, multiomics mode is used.

Usage:

$ seqnado config [OPTIONS] [ASSAY]

Arguments:

  • [ASSAY]: rna, atac, snp, chip, cat, meth, mcc, crispr, multiomics. If omitted, multiomics mode is used.

Options:

  • --make-dirs / --no-make-dirs: Create/don't create the output project directory or fastq subdir. [default: make-dirs]
  • --render-options / --no-render-options: Render all options (even if not used by the workflow). [default: no-render-options]
  • -o, --output PATH: Explicit path for the rendered config file.
  • -v, --verbose: Increase logging verbosity.
  • --interactive / --no-interactive: Interactively prompt for config values. Non-interactive mode only works for single assay configs (except MCC and multiomics). [default: interactive]
  • --help: Show this message and exit.

seqnado tools

List and explore bioinformatics tools available in the SeqNado pipeline.

Usage:

$ seqnado tools [OPTIONS] [TOOL]

Arguments:

  • [TOOL]: Specific tool name to get help for (e.g., fastqc, deeptools)

Options:

  • -l, --list: List all available tools with descriptions.
  • -c, --category TEXT: Filter tools by category name or number. Use without a value to interactively select a category.
  • --options: Show tool options/help from the container (requires tool name and apptainer).
  • --citation: Show the BibTeX citation for a tool (requires tool name).
  • -s, --subcommand TEXT: Specify a tool subcommand for help (e.g. plotHeatmap).
  • -v, --verbose: Increase logging verbosity.
  • --help: Show this message and exit.

seqnado download

Download FASTQ files from GEO/SRA using a metadata TSV file and optionally generate a design file.

Usage:

$ seqnado download [OPTIONS] METADATA_TSV

Arguments:

  • METADATA_TSV: TSV file from GEO/ENA with columns: run_accession, sample_title, library_name, and library_layout (PAIRED or SINGLE). [required]

Options:

  • -o, --outdir PATH: Output directory for downloaded FASTQ files. [default: fastqs]
  • -a, --assay TEXT: Assay type for generating design file after download. If not provided, only downloads FASTQs.
  • -d, --design-output PATH: Output path for design CSV (default: metadata_{assay}.csv in outdir).
  • -c, --cores INTEGER: Number of parallel download jobs. [default: 4]
  • --preset [lc|le|ls|ss|t]: Snakemake job profile preset for downloads. [default: le]
  • -n, --dry-run: Show what would be downloaded without downloading.
  • -v, --verbose: Increase logging verbosity.
  • --help: Show this message and exit.

seqnado design

Generate a SeqNado design CSV from FASTQ files for ASSAY. If no assay is provided, multiomics mode is used.

Usage:

$ seqnado design [OPTIONS] [ASSAY] [FASTQ ...]

Arguments:

  • [ASSAY]: Assay type. Options: rna, atac, snp, chip, cat, meth, mcc, crispr, multiomics. If omitted, multiomics mode is used.
  • [FASTQ ...]

Options:

  • -o, --output PATH: Output CSV filename (default: metadata_{assay}.csv).
  • --ip-to-control TEXT: List of antibody,control pairings for IP assays (e.g. ChIP). Format: 'antibody1:control1,antibody2:control2' If provided will assign a control with a specified name to that ip in the metadata. If not provided, controls will be assigned based on a best-effort matching of sample names.
  • --group-by: Group samples by a regular expression or a column.
  • --auto-discover / --no-auto-discover: Search common folders if none provided. [default: auto-discover]
  • --interactive / --no-interactive: Interactively offer to add missing columns using schema defaults. [default: interactive]
  • --accept-all-defaults: Non-interactive: auto-add only columns that have a schema default.
  • --deseq2-pattern TEXT: Regex pattern to extract DESeq2 groups from sample names. First capture group will be used. Example: r'-(\w+)-rep' for 'sample-GROUP-rep1'
  • -v, --verbose: Increase logging verbosity.
  • --help: Show this message and exit.

seqnado pipeline

Run the data processing pipeline for ASSAY (Snakemake under the hood). Any additional arguments are passed to Snakemake (e.g., seqnado pipeline rna -n for dry-run, --unlock, etc.).

Usage:

$ seqnado pipeline [OPTIONS] [ASSAY]

Arguments:

  • [ASSAY]: Assay type (required for single-assay, optional for Multiomic mode)

Options:

  • --configfile PATH: Path to a SeqNado config YAML (default: config_<ASSAY>.yaml).
  • --version: Print SeqNado version and exit.
  • --preset [lc|le|ls|ss|t]: Snakemake job profile preset. [default: le]
  • --clean-symlinks / --no-clean-symlinks: Remove symlinks created by previous runs. [default: no-clean-symlinks]
  • -s, --scale-resources FLOAT: Scale memory/time (env: SCALE_RESOURCES). [default: 1.0]
  • -v, --verbose: Increase logging verbosity.
  • -q, --queue TEXT: Slurm queue/partition for the ss preset. [default: short]
  • --print-cmd: Print the Snakemake command before running it.
  • --help: Show this message and exit.