Parameters
Path to YAML file containing information about the dataset
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.
pattern: ^\S+\.yaml$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Email address for completion summary.
Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Kmer size to use for all kmer-based subroutines in the Kmer profiling subworkflow. This parameter is overridden by the provided kmer size for a given input read set if a FastK database is provided.
default: 31If Hi-C data is provided, enabling this will produce a Hi-C phased assembly with hifiasm.
If parental read data is provided, enabling this will produce a trio binned assembly with hifiasm.
Options controlling Hifiasm error correction.
See the "Error correction options" section of https://hifiasm.readthedocs.io/en/latest/parameter-reference.html for options.
Options controlling Hifiasm assembly output, including those affecting assemblty, purging, phasing and trio binning.
See https://hifiasm.readthedocs.io/en/latest/parameter-reference.html for options.
A comma-separated list defining which types of assemblies to purge. Must draw from the options "primary", "hic_phased", or "trio_binned".
default: 'primary'During haplotype purging, look in the middle of contigs for potential haplotigs. This removes the "-e" option from the purgedups/getseqs command.
Manually override the cutoffs set by purge_dups/calcuts. Must be a comma-separated string with three coverage cutoffs - low, medium, and high - for example. "5,20,100".
Number of chunks to split assembly into for polishing.
default: 100Parameters used to describe centralised config profiles. These should not be edited.
The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.
Git commit id for Institutional configs.
default: 'master'Base directory for Institutional configs.
default: 'https://raw.githubusercontent.com/nf-core/configs/master'If 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.
Less common options for the pipeline, typically set in a config file.
These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.
Typically these options would be set in a Nextflow config file loaded for all pipeline runs, such as ~/.nextflow/config.
Method used to save pipeline results to output directory.
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.
Email address for completion summary, only when pipeline fails.
An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Incoming hook URL for messaging service
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
default: 1Base URL or local path to location of pipeline test dataset files
default: 'https://raw.githubusercontent.com/nf-core/test-datasets/'