schema.md

. 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

Other parameters

Parameter	Description	Type	Default	Required	Hidden
samplesheet	samplesheet	string	''	True
enable_conda	use conda (not supported)	boolean
collect	combine reads from multiple fastq files into one?	boolean
skip_flye	skip flye assembly	boolean
skip_alignments	skip alignment to initial assembly and reference	boolean
flye_mode	flye mode to use	string	'--nano-hq'
flye_args	extra args for flye	string	''
polish_pilon	use pilon to polish with short reads	boolean
medaka_model	medaka model to use	string	'[email protected]:consesus'
lift_annotations	run liftoff to lift over annotations	boolean
out	results directory	string	'./out'
scaffold_ragtag	Scaffold with ragtag	boolean
scaffold_links	Scaffold with links	boolean
scaffold_longstitch	Scaffold with longstitch	boolean
busoc_db	path to busco db	string	/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/software/busco_db
porechop	run porechop	boolean
use_ref	Use a reference genome	boolean	True
busco_lineage	busco lineage to use	string	"brassicales_odb10"
jelly_is_reads	not used	string			True
kmer_length	k-mer length	integer	21
read_length	read length (if null, estimate)	integer
dump	Dump kmers from jellyfish	boolean
genome_size	Expected genome size, if null estimate from kmers	integer
hifi	HiFi reads available?	boolean
lima	Use lima on hifi reads	boolean
pacbio_primers	File containing pacbio primers	string
hifi_ont	Merge hifi and ont reads	boolean
hifi_only	Only hifi reads	boolean
hifi_args	Extra arguments for hifiasm	string
polish_medaka	polish with medaka	string