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...benchmark: Aggregate Snakemake .benchmark TSV files...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). With --fill-missing, --no-interactive writes a hand-editable scaffold instead of prompting. [default: interactive]--fill-missing <path>: Load an existing config YAML and fill in optional sections that were left null (hub, bigwigs, plotting, spikein, peak_calling, snp_calling, methylation) — e.g. because a hub wasn't selected the first time round. Ignores ASSAY (derived from the file). Overwrites in place unless -o/--output or --new-file is given.--new-file: With --fill-missing, write the result to '<name>.filled.yaml' instead of overwriting the input. Ignored if -o/--output is given.--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 <str>: 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 <str>: 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 <str>: 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 <int>: Number of cores/parallel jobs. [default: 4]--preset <function>: 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 <str>: 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.--consensus-by, --group-by <str>: Populate 'consensus_group' from an existing column name or a regex extracted from sample names. e.g. '--consensus-by ip' groups ChIP-seq/CUT&Tag samples by antibody for consensus peak calling/counting.--condition-by <str>: Populate 'condition' from an existing column name or a regex extracted from sample names. e.g. '--condition-by "-(control|treated)-"' extracts the condition from sample names for bigwig comparisons.--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 <str>: 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 <function>: 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 <str>: Slurm queue/partition for thesspreset. [default: short]--print-cmd: Print the Snakemake command before running it.--help: Show this message and exit.
seqnado benchmark¶
Aggregate Snakemake .benchmark TSV files into a summary TSV and HTML report.
Usage:
Arguments:
[BENCHMARK_DIR]: Directory containing benchmark TSV files or a SeqNado output root. Defaults to .benchmark. [default: .benchmark]
Options:
-o, --html <path>: Path to write the HTML report. Defaults to seqnado_output/seqnado_benchmark.html when available. [default: benchmark_report.html]--tsv <path>: Path to write the aggregated benchmark table. Defaults to seqnado_output/seqnado_benchmark.tsv when available. [default: benchmark_summary.tsv]--top <int range>: Number of longest and highest-memory jobs to highlight in the HTML report. [default: 20; x>=1]-v, --verbose: Increase logging verbosity.--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 <str>: 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 <str>: Spike-in genome name for composite builds (e.g., mm39)--fasta <path>: Custom FASTA file for the primary genome, instead of downloading from UCSC (single genome only)--gtf <path>: Custom GTF file for the primary genome, instead of downloading from UCSC (single genome only)--spikein-fasta <path>: Custom FASTA file for the --spikein genome, instead of downloading from UCSC--spikein-gtf <path>: Custom GTF file for the --spikein genome, instead of downloading from UCSC--preset <function>: Snakemake job profile preset. [default: le]--profile, --profiles <path>: Path to a Snakemake profile directory (overrides --preset).-c, --cores <int>: 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 <int>: 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.