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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Optional Profiles¶

You can use execution profiles to control behavior, e.g.:

nextflow run main.nf -profile docker

Available Profiles¶

• docker: Runs processes inside Docker containers using the specified image.
• singularity: Runs in Singularity containers (if configured).
• local: Default execution on local machine without containers.

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Custom Configuration¶

To override parameters, use -params-file:

nextflow run main.nf -params-file custom_params.json

Example custom_params.json:

{
  "reads": "data/*.fq.gz",
  "reference": "data/NC_045512.2.fasta",
  "threads": 16
}

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