Repeat Parameters

Automatically generated from the pipeline nextflow_schema.json.

Input/output options

Define where the pipeline should find input data, write results, and cache downloaded files.

Parameter	Type	Default	Required	Description
csvFile	string		yes	Path to the input CSV metadata file.
outdir	string	./results	yes	Output directory.
tracedir	string	./results/pipeline_info	no	Directory for execution reports and trace files.
cacheDir	string	./results/cache	no	Directory used by cached fetch steps.
files_latency	integer	60	no	Sleep time in seconds after file-publishing steps.
cleanup	boolean	True	no	Remove temporary files when supported.
cleanCache	boolean	False	no	Remove cached downloaded files after the run.

Repeat analysis options

Enable repeat annotation steps and configure repeat tools.

Parameter	Type	Default	Required	Description
generate_lib	boolean	False	no	Check for an existing RepeatModeler library and generate one when it is missing.
run_repeatmasker	boolean	False	no	Run RepeatMasker using the RepeatModeler library channel.
run_red	boolean	False	no	Run RED on the fetched genome assembly.
run_dust	boolean	False	no	Run DustMasker on the fetched genome assembly.
run_trf	boolean	False	no	Run TRF on the fetched genome assembly.
ncbiBaseUrl	string	https://api.ncbi.nlm.nih.gov/datasets/v2alpha/genome/accession/	no	NCBI datasets API base URL used for genome downloads.
repeats_ftp_base	string	http://ftp.ebi.ac.uk/pub/databases/ensembl/repeats/unfiltered_repeatmodeler/species/	no	Base URL for pre-computed RepeatModeler libraries.
repeatmasker_path	string		no	Path to the RepeatMasker executable.
builddatabase_path	string		no	Path to the BuildDatabase executable.
engine_repeatmasker	string	rmblast	no	RepeatMasker search engine.
engine_repeatmodeler	string	ncbi	no	RepeatModeler search engine.
red_path	string		no	Path to the RED executable.
dust_path	string		no	Path to the DustMasker executable.
trf_path	string		no	Path to the TRF executable.
trf_match_score	integer	2	no	TRF match score.
trf_mismatch_score	integer	5	no	TRF mismatch penalty.
trf_delta	integer	7	no	TRF indel penalty.
trf_pm	integer	80	no	TRF match probability.
trf_pi	integer	10	no	TRF indel probability.
trf_minscore	integer	40	no	TRF minimum alignment score to report.
trf_maxperiod	integer	500	no	TRF maximum period size.