Parameters
Input YAML specifying the location of all genomic data for assembly. See the documentation for a full specification.
YAML file specifying the parameters for a set of assemblies, including datasets and arguments. See the documentation for a full specification.
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: 31Save the FastK databases generated by the pipeline to the output directory.
How many reads to map in a single chunk when mapping reads to the primary assembly during purging.
default: 500000Which minimap2 mapping mode to use when mapping ONT? See https://lh3.github.io/minimap2/minimap2.html for a full list.
default: 'map-ont'Path to a container with longranger to use for the longranger processes. Required for polishing to run.
Number of chunks to split assembly into for polishing.
default: 100Options to control the mapping of Hi-C reads and scaffolding of an assembly.
Number of CRAM slices to include per CRAM file per mapping chunk. Lower values mean more Hi-C mapping jobs are spawned, but each should have a lower run time.
default: 10000Minimum MapQ score for a Hi-C read to be retained for scaffolding.
default: 10Bin size to use when building cooler contact maps.
default: 1000Parameters to configure the assembly QC steps that run for each assembly generated.
Path to a local directory containing pre-downloade BUSCO lineages.
Lineage datasets can be downloaded using busco --download.
The minimum size of a reference organellar genome to use in reference-based organelle assembly with Mitohifi
default: 15000Parameters 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/'Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.