Parameters

Input/output options

Define where the pipeline should find input data and save output data.

--input

type: 'string'

Path to comma-separated file containing information about the samples in the experiment.

required

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$

--binsize

type: 'integer'

Bin size in base pairs for cooler cload

default: 1000
required

--kmer_size

type: 'integer'

Size for Fastk to create the k-mer library

default: 31
required

--assembly

type: 'string'

The Genbank assembly accession for the assembly, for example: GCA_922984935.2.

required

--biosample_wgs

type: 'string'

The biosample accesion(s) linked to the WGS samples in the experiment, for example: SAMEA7520803.

required

--biosample_rna

type: 'string'

The biosample accesion(s) linked to the RNA samples in the experiment, for example: SAMEA7521081.

--biosample_hic

type: 'string'

The biosample accesion(s) linked to the Hi-C samples in the experiment, for example: SAMEA7520846.

--outdir

type: 'string'

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

default: 'results'
required

--email

type: 'string'

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_title

type: 'string'

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

--cool_order

type: 'string'

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.

--write_to_portal

type: 'boolean'

Flag to control if results are written to genome notes portal database .

hidden

--genome_notes_api

type: 'string'

URL for Genome Notes Portal API .

--note_template

type: 'string'

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

--upload_higlass_data

type: 'boolean'

flag to control if Higlass server should be updated to add new files

hidden

--higlass_url

type: 'string'

URL for the Higlass server

hidden

--higlass_upload_directory

type: 'string'

The ingress directory for the kubernetes cluster running the HiGlass server.

hidden

--higlass_data_project_dir

type: 'string'

Subdirectory struture to use for organising HiGlass data, suggested format is / e.g. '/asg/algae'

hidden

--higlass_kubeconfig

type: 'string'

The path to the kubeconfig for the kubernetes cluster running the HiGlass server.

hidden

--higlass_deployment_name

type: 'string'

Name of the kubernetes deployment for the HiGlass server.

hidden

--higlass_namespace

type: 'string'

The name for the namespace used in the Kubernetes cluster running the HiGlass server.

hidden

Databases

Define where the pipeline should find databases.

--lineage_db

type: 'string'

Local directory where clade-specific BUSCO lineage datasets are stored.

--lineage_tax_ids

type: 'string'

Local file that holds a mapping between BUSCO lineages and taxon IDs.

Reference genome options

Reference genome related files and options required for the workflow.

--fasta

type: 'string'

Path to FASTA genome file.

required

Execution

Control the execution of the pipeline.

hidden

--use_work_dir_as_temp

type: 'boolean'

Set to true to make tools (e.g. sort, FastK, MerquryFK) use the work directory for their temporary files, rather than the system default.

hidden

Institutional config options

Parameters used to describe centralised config profiles. These should not be edited.

hidden

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.

--custom_config_version

type: 'string'

Git commit id for Institutional configs.

default: 'master'
hidden

--custom_config_base

type: 'string'

Base directory for Institutional configs.

default: 'https://raw.githubusercontent.com/nf-core/configs/master'
hidden

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.

--config_profile_name

type: 'string'

Institutional config name.

hidden

--config_profile_description

type: 'string'

Institutional config description.

hidden

--config_profile_contact

type: 'string'

Institutional config contact information.

hidden

--config_profile_url

type: 'string'

Institutional config URL link.

hidden

Max job request options

Set the top limit for requested resources for any single job.

hidden

If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.

Note that you can not increase the resources requested by any job using these options. For that you will need your own configuration file. See the nf-core website for details.

--max_cpus

type: 'integer'

Maximum number of CPUs that can be requested for any single job.

default: 16
hidden

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

--max_memory

type: 'string'

Maximum amount of memory that can be requested for any single job.

default: '128.GB'
hidden

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

--max_time

type: 'string'

Maximum amount of time that can be requested for any single job.

default: '240.h'
hidden

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

pattern: ^(\d+\.?\s*(s|m|h|day)\s*)+$

Generic options

Less common options for the pipeline, typically set in a config file.

hidden

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.

--help

type: 'boolean'

Display help text.

hidden

--version

type: 'boolean'

Display version and exit.

hidden

--publish_dir_mode

type: 'string'

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_on_fail

type: 'string'

Email address for completion summary, only when pipeline fails.

hidden

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})$

--plaintext_email

type: 'boolean'

Send plain-text email instead of HTML.

hidden

--max_multiqc_email_size

type: 'string'

File size limit when attaching MultiQC reports to summary emails.

default: '25.MB'
hidden

--monochrome_logs

type: 'boolean'

Do not use coloured log outputs.

hidden

--hook_url

type: 'string'

Incoming hook URL for messaging service

hidden

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

--multiqc_config

type: 'string'

Custom config file to supply to MultiQC.

hidden
type: 'string'

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden

--multiqc_methods_description

type: 'string'

Custom MultiQC yaml file containing HTML including a methods description.

hidden

--tracedir

type: 'string'

Directory to keep pipeline Nextflow logs and reports.

default: '${params.outdir}/pipeline_info/genomenote'
hidden

--validate_params

type: 'boolean'

Boolean whether to validate parameters against the schema at runtime

default: 1
hidden

--show_hidden_params

type: 'boolean'

Show all params when using --help

hidden

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

The following uncommon parameters have been hidden: --write_to_portal, --upload_higlass_data, --higlass_url, --higlass_upload_directory, --higlass_data_project_dir, --higlass_kubeconfig, --higlass_deployment_name, --higlass_namespace, --use_work_dir_as_temp, --custom_config_version, --custom_config_base, --config_profile_name, --config_profile_description, --config_profile_contact, --config_profile_url, --max_cpus, --max_memory, --max_time, --help, --version, --publish_dir_mode, --email_on_fail, --plaintext_email, --max_multiqc_email_size, --monochrome_logs, --hook_url, --multiqc_config, --multiqc_logo, --multiqc_methods_description, --tracedir, --validate_params, --show_hidden_params

to show all hidden params.