nf-core/createpanelrefs
Generate Panel of Normals, models or other similar references from lots of samples
Options used by the germlinecnvcaller subworkflow
Specifies which analysis type for the pipeline- either 'wgs' or 'wes'.
stringLength (in bp) of the bins. If zero, no binning will be performed.
number1000Used by GATK's PreprocessIntervals. GATK recommends a bin length of 1000 for WGS analysis, and 0 for WES analysis.
Path to directory for a bed file containing regions to be exluded from the analysis.
string^\S+\.bed$If the regions you would like to exclude are in bed format, use this option. If you have an interval_list file, use exclude_interval_list parameter instead.
Path to directory for exclude_interval_list file.
string^\S+\._interval_list$If the regions you would like to exclude are in interval_list format, use this option. If you have a bed file, use exclude parameter instead.
Path to Umap single-read mappability track in .bed or .bed.gz format. Overlapping intervals must be merged.
stringUsed by GATK's AnnotateIntervals.
Length (in bp) of the padding regions on each side of the intervals.
numberUsed by GATK's PreprocessIntervals. GATK recommends a padding of 0 for WGS analysis, and 250 for WES analysis.
Name for panel of normals.
stringgermlinecnvcallerPath to a file containing ploidy priors table.
stringUsed by GATK's DeterminGermlineContigPloidy.
Output file format for count data
stringWhen scattering with this argument, each of the resultant files will (ideally) have this amount of interval-counts.
number5000Used by GATK/Picards's IntervalListTools.
Path to segmental-duplication track in .bed or .bed.gz format. Overlapping intervals must be merged.
stringUsed by GATK's AnnotateIntervals.
Path to directory for target bed file.
string^\S+\.bed$If the regions you would like to analyse are in bed format, use this option. If you have an interval_list file, use target_interval_list parameter instead.
Path to directory for target interval_list file.
string^\S+\._interval_list$If the regions you would like to analyse are in interval_list format, use this option. If you have a bed file, use target_bed parameter instead.
Options used by the gens subworkflow
Length (in bp) of the bins. If zero, no binning will be performed.
number100Used by GATK's PreprocessIntervals. We recommend a bin length of 100.
Name for panel of normals.
stringgensOutput file format for count data
stringOptions used by the cnvkit subworkflow
stringOptions used by the mutect2 subworkflow
stringPath to target bed file
string^\S+\.bed$Define where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
undefinedA design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See usage docs.
If no input file is specified, sarek will attempt to locate one in the {outdir} directory.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringMost common options used for the pipeline
Tools to use for building Panel of Normals or models.
stringMultiple tools separated with commas.
Tools available: CNVKIT,germlinecnvcaller,gens,mutect2
This parameter must be a combination of the following values:cnvkit, germlinecnvcaller, gens, mutect2Reference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf 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.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Path to sequence dictionary file
string^\S+\.dict$Path to fasta index file
string^\S+\.fn?a(sta)?\.fai$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy 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.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.