. pipeline parameters

Generic options

Less common options for the pipeline, typically set in a config file.

Parameter	Description	Type	Default	Required	Hidden
`publish_dir_mode`	Method used to save pipeline results to output directory. Help The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.	`string`	copy		True

Parameter	Type	Default
`samplesheet`	`string`	None
`enable_conda`	`string`	None
`collect`	`string`	None
`skip_flye`	`string`	None
`skip_alignments`	`string`	None
`flye_mode`	`string`	None
`flye_args`	`string`	None
`polish_pilon`	`string`	None
`medaka_model`	`string`	None
`lift_annotations`	`string`	None
`out`	`string`	None
`scaffold_ragtag`	`string`	None
`scaffold_links`	`string`	None
`scaffold_slr`	`string`	None