Pipeline Parameters¶

This section lists the configurable parameters used in the pipeline. These can be adjusted using a custom configuration file or passed directly via the command line.

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Core Parameters¶

Parameter	Default	Description
reads	*.fastq.gz	Glob pattern to match input FASTQ files
reference	reference.fasta	Reference genome in FASTA format
threads	8	Number of threads to use for multithreaded tools

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Default Configuration¶

nextflow run main.nf -with-conda

💡 All parameters can also be set directly via -params flag or in nextflow.config.