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.
number1000Length (in bp) of the padding regions on each side of the intervals.
numberName for panel of normals.
stringgermlinecnvcallerOutput file format for count data
stringWhen scattering with this argument, each of the resultant files will (ideally) have this amount of interval-counts.
number5000Options used by the gens subworkflow
Length (in bp) of the bins. If zero, no binning will be performed.
number100Maximum chunk size when writing the HDF5 file
number167772150Minimum interval median percentile for gatk CreateReadCountPanelOfNormals
number5Name for panel of normals.
stringgensOutput file format for count data
stringOptions used by the cnvkit subworkflow
Path to directory for target file.
stringOptions used by the mutect2 subworkflow
Name for panel of normals.
stringDefine where the pipeline should find input data and save output data.
Path to comma-separated file containing information about the samples in the experiment.
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})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringMost common options used for the pipeline
Tools to use for building Panel of Normals or models.
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to sequence dictionary file
string^\S+\.dict$Path to fasta index file
string^\S+\.fn?a(sta)?\.fai$Path to GENS interval list file
string^\S+\.interval_list$Path to directory for a bed file containing regions to be exluded from the analysis.
string^\S+\.bed$Path to directory for exclude_interval_list file.
string^\S+\.interval_list$Path to Umap single-read mappability track in .bed or .bed.gz format. Overlapping intervals must be merged.
stringPath to a file containing ploidy priors table.
stringPath to segmental-duplication track in .bed or .bed.gz format. Overlapping intervals must be merged.
stringPath to directory for target bed file.
string^\S+\.bed$Path to directory for target interval_list file.
string^\S+\.interval_list$Path to target bed file
string^\S+\.bed$Do not load the iGenomes reference config.
booleanThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/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/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringCustom 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
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://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.
string