primerlab run

CLI reference for the primerlab run command

Run a primer design workflow.

Synopsis

primerlab run <workflow> [options]

Arguments

Argument	Required	Description
workflow	Yes	Workflow type: pcr, qpcr, or crispr

Options

Option	Short	Description
--config	-c	Path to configuration YAML file
--out	-o	Override output directory
--debug		Enable debug logging
--dry-run		Validate config without running
--export	-e	Export formats (comma-separated)
--mask	-m	Region masking mode
--quiet	-q	Suppress warnings (v0.1.6)
--validate	-V	Run in-silico PCR validation (v0.2.3)
--blast		Run off-target check (v0.3.1)
--blast-db		Path to BLAST database
--report	-R	Generate enhanced report (v0.3.3)
--report-format		Report format: markdown, html, json
--report-output		Report output path

Examples

Basic PCR Design

primerlab run pcr --config my_pcr.yaml

qPCR with TaqMan Probe

primerlab run qpcr --config my_qpcr.yaml

With Masking

# Auto-detect lowercase and N-masked regions
primerlab run pcr --config my_pcr.yaml --mask auto

Export to Multiple Formats

primerlab run pcr --config my_pcr.yaml --export idt,benchling

Quiet Mode (v0.1.6)

# Suppress warnings for scripted pipelines
primerlab run pcr --config my_pcr.yaml --quiet

Dry Run

# Validate config without running
primerlab run pcr --config my_pcr.yaml --dry-run

With In-silico Validation (v0.2.3)

# Design + validate primers against template
primerlab run pcr --config my_pcr.yaml --validate

With BLAST Off-target Check (v0.3.1)

# Design + check off-targets
primerlab run pcr --config my_pcr.yaml --blast --blast-db genome.fasta

With Report Generation (v0.3.3)

# Generate enhanced HTML report
primerlab run pcr --config my_pcr.yaml --report --report-format html --report-output report.html

Mask Modes

Mode	Description
auto	Detect both lowercase and N-masked regions
lowercase	Only detect lowercase (RepeatMasker) regions
n	Only detect N-masked regions
none	No masking (default)

Export Formats

Format	Description
idt	IDT ordering format
sigma	Sigma-Aldrich format
thermo	Thermo Fisher format
benchling	Benchling CSV import
xlsx	Excel spreadsheet