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:
Options:
-v, --version: Show version and exit.--verbose: Enable verbose logging (DEBUG level).--help: Show this message and exit.
Commands:
init: Initialize SeqNado user environment.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...genomes: Manage genome configurations
seqnado init¶
Initialize SeqNado user environment.
- Logs the current Conda environment if active (optional).
- Runs packaged Apptainer/Singularity init (if
apptaineron PATH). - Ensures ~/.config/seqnado/genome_config.json exists (template or preset).
Usage:
Options:
--preset / --no-preset: Use packaged preset genomes instead of the editable template. [default: no-preset]-n, --dry-run: Show actions without executing them.-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:
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:
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:
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 cores/parallel jobs. [default: 4]--preset [a|lc|ld|le|ls|ss|t]: Snakemake job profile preset. [default: le]--profile, --profiles PATH: Path to a Snakemake profile directory (overrides --preset).-n, --dry-run: Show actions without executing them.-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:
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 TEXT: Group samples by a regular expression or a column name.--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:
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 [a|lc|ld|le|ls|ss|t]: Snakemake job profile preset. [default: le]--profile, --profiles PATH: Path to a Snakemake profile directory (overrides --preset).--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 thesspreset. [default: short]--print-cmd: Print the Snakemake command before running it.--help: Show this message and exit.
seqnado genomes¶
Manage genome configurations
Usage:
Options:
--help: Show this message and exit.
Commands:
list: Show packaged and user genome presets.edit: Open user genome config in $EDITOR.build: Download genome and build indices via...fastqscreen: Generate FastqScreen configuration file.
seqnado genomes list¶
Show packaged and user genome presets.
Usage:
Arguments:
[ASSAY]: Assay type. Options: rna, atac, snp, chip, cat, meth, mcc, crispr, multiomics [default: atac]
Options:
-v, --verbose: Increase logging verbosity.--help: Show this message and exit.
seqnado genomes edit¶
Open user genome config in $EDITOR.
Usage:
Options:
-v, --verbose: Increase logging verbosity.--help: Show this message and exit.
seqnado genomes build¶
Download genome and build indices via Snakemake.
Usage:
Options:
-g, --name TEXT: Genome name(s), comma-separated for multiple (e.g., hg38 or hg38,mm39,dm6) [required]-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 [a|lc|ld|le|ls|ss|t]: Snakemake job profile preset. [default: le]--profile, --profiles PATH: Path to a Snakemake profile directory (overrides --preset).-c, --cores INTEGER: Number of cores/parallel jobs. [default: 4]--scale-resources FLOAT: Scale memory/time (for build subcommand). [default: 1.0]-n, --dry-run: Show actions without executing them.-v, --verbose: Increase logging verbosity.--help: Show this message and exit.
seqnado genomes fastqscreen¶
Generate FastqScreen configuration file.
Usage:
Options:
-s, --screen PATH: Output path for fastqscreen config (default: ~/.config/seqnado/fastq_screen.conf)-t, --threads INTEGER: Number of threads for Bowtie2 [default: 8]--no-contaminants: Exclude contaminant databases--contaminant-path PATH: Path to contaminant reference files-v, --verbose: Increase logging verbosity.--help: Show this message and exit.