Parameters
Path to comma-separated file containing information about the samples in the experiment.
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.
pattern: ^\S+\.csv$The busco lineage used for ancestral painting (must match --ancestral_table).
The Genbank assembly accession for the assembly, for example: GCA_922984935.2.
The biosample accesion(s) linked to the WGS samples in the experiment, for example: SAMEA7520803.
The biosample accesion(s) linked to the RNA samples in the experiment, for example: SAMEA7521081.
The biosample accesion(s) linked to the Hi-C samples in the experiment, for example: SAMEA7520846.
Select which contact maps should be generated, higlass, pretext, or all
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
default: 'results'Non-empty string used as the suffix and output directory name for merged data files
default: 'merge'Defines the suffix added to merged file names and name of output directory when multiple read files that share the same specimen are merged. Allowed characters are letters, numbers, dot (.), underscore (_), and hyphen (-).
pattern: ^[A-Za-z0-9._-]+$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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
Path to a file that contains the sequence names in the order you want to represent them on the contact-map.
If not specified, the pipeline will use the sequences in the same order they are listed by the NCI, which follows the karyotype.
The path to a genome note template file.
Set this parameter if you have a genome note template file that you wish to populate. Templates may be docx or xml files
Local file that holds a mapping between BUSCO lineages and taxon IDs.
Set to true to make tools (e.g. sort, FastK, MerquryFK) use the work directory for their temporary files, rather than the system default.
Parameters 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})$File size limit when attaching MultiQC reports to summary emails.
default: '25.MB'Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
Custom MultiQC yaml file containing HTML including a methods description.
Boolean whether to validate parameters against the schema at runtime
default: trueBase 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.