Parameters

Note

Parameter validation and help are driven by nextflow_schema.json using the nf-schema plugin in main.nf and nextflow.config.

Tip

Regenerate parameter documentation from schema whenever parameter definitions change.

Parameter	Type	Default	Description
input	string	data/input.fasta	Path to input DNA multi-FASTA file (up to 1000 headers).
outdir	string	results	Output directory for final and intermediate pipeline results.
max_cpus	integer	96	Maximum CPUs available to the pipeline executor.
max_memory	string	1000.GB	Maximum memory available to pipeline processes.
max_time	string	240.h	Maximum walltime available to pipeline processes.
help	boolean	false	Print help text generated by nf-schema plugin.

Parameter DAG context

flowchart LR
    A[input] --> B[SPLIT_FASTA]
    C[max_cpus/max_memory/max_time] --> D[Process resources]
    E[outdir] --> F[publishDir targets]