parameters.md

birneylab/varexplore pipeline parameters

Explore genetic variants linked around a variant of interest for low-coverage sequencing data

Input/output options

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

Parameter	Description	Type	Default	Required	Hidden
input	Path to comma-separated file containing information about the samples in the experiment.	string
variant_table	Path to comma-separated file containing information about the genetic variants to be considered.	string
vcf	VCF(.gz) file with samples overlapping with the ones in input Help This is needed for extracting the sample genotypes at the variants of interest.	string
outdir	The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.	string		True
email	Email address for completion summary. Help 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.	string

Reference genome options

Reference genome related files and options required for the workflow.

Parameter	Description	Type	Default	Required	Hidden
genome	Name of iGenomes reference. Help If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38. See the nf-core website docs for more details.	string
fasta	Path to FASTA genome file. Help This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.	string
igenomes_base	Directory / URL base for iGenomes references.	string	s3://ngi-igenomes/igenomes
igenomes_ignore	Do not load the iGenomes reference config. Help Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.	boolean

ENSEMBL VEP Options

Information needed for predicting variant effects with VEP

Parameter	Description	Type	Default	Required	Hidden
vep_genome	VEP genome	string		True
vep_species	VEP species	string		True
vep_cache_version	VEP cache version	string		True

Institutional config options

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

Parameter	Description	Type	Default	Required	Hidden
custom_config_version	Git commit id for Institutional configs.	string	master		True
custom_config_base	Base directory for Institutional configs. Help 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.	string	https://raw.githubusercontent.com/nf-core/configs/master		True
config_profile_name	Institutional config name.	string			True
config_profile_description	Institutional config description.	string			True
config_profile_contact	Institutional config contact information.	string			True
config_profile_url	Institutional config URL link.	string			True

Max job request options

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

Parameter	Description	Type	Default	Required	Hidden
max_cpus	Maximum number of CPUs that can be requested for any single job. Help Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1	integer	16		True
max_memory	Maximum amount of memory that can be requested for any single job. Help 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'	string	128.GB		True
max_time	Maximum amount of time that can be requested for any single job. Help 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'	string	240.h		True

Generic options

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

Parameter	Description	Type	Default	Required	Hidden
help	Display help text.	boolean			True
version	Display version and exit.	boolean			True
publish_dir_mode	Method used to save pipeline results to output directory. Help 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.	string	copy		True
email_on_fail	Email address for completion summary, only when pipeline fails. Help An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.	string			True
plaintext_email	Send plain-text email instead of HTML.	boolean			True
monochrome_logs	Do not use coloured log outputs.	boolean			True
hook_url	Incoming hook URL for messaging service Help Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.	string			True
validate_params	Boolean whether to validate parameters against the schema at runtime	boolean	True		True
validationShowHiddenParams	Show all params when using --help Help 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.	boolean			True
validationFailUnrecognisedParams	Validation of parameters fails when an unrecognised parameter is found. Help By default, when an unrecognised parameter is found, it returns a warinig.	boolean			True
validationLenientMode	Validation of parameters in lenient more. Help Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.	boolean			True