nf-core/genomeassembler
Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Options controlling pipeline behavior
use reference genome
booleantrueskip assembly steps
booleanSkip assembly and perform only qc.
skip alignments during qc
booleanOptions for ONT reads
ONT reads available?
booleancollect ONT reads into a single file
booleanrun porechop on ONT reads
booleanread length for genomescope (ONT only)
integerrun jellyfish on ONT reads to compute k-mer distribution and estimate genome size
booleantruedump jellyfish output
booleankmer length to be used for jellyfish
integer21Options for HiFi reads
HiFi reads available?
booleanrun lima on HiFi reads?
booleanfile containing pacbio primers for trimming with lima
stringOptions controlling assembly
Assembler to use. Valid choices are: 'hifiasm', 'flye', or 'flye_on_hifiasm'. flye_on_hifiasm will scaffold flye assembly (ont) on hifiasm (hifi) assembly using ragtag
stringexpected genome size, optional
integerflye mode
stringadditional args for flye
stringUse hifi and ONT reads with hifiasm --ul
booleanExtra arguments passed to hifiasm
stringOptions for short reads
Short reads available?
booleantrim short reads with trimgalore
booleantruekmer length for meryl / merqury
integer21Polishing options
Polish assembly with pilon? Requires short reads
booleanPolish assembly with medaka (ONT only)
booleanmodel to use with medaka
stringScaffolding options
Scaffold with longstitch?
booleanScaffolding with links?
booleanScaffold with ragtag (requires reference)?
booleanOptions for QC tools
Run merqury
booleantrueLong reads that should be used for QC when both ONT and HiFi reads are provided. Options are 'ONT' or 'HIFI'
stringRun BUSCO?
booleantruePath to busco db (optional)
stringBusco lineage to use
stringbrassicales_odb10Run quast
booleantrueOptions controlling annotation liftover
Lift-over annotations (requires reference)?
booleantrue