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’.
string
Length (in bp) of the bins. If zero, no binning will be performed.
number
1000
Length (in bp) of the padding regions on each side of the intervals.
number
Name for panel of normals.
string
germlinecnvcaller
Output file format for count data
string
When scattering with this argument, each of the resultant files will (ideally) have this amount of interval-counts.
number
5000
Options used by the gens subworkflow
Length (in bp) of the bins. If zero, no binning will be performed.
number
100
Maximum chunk size when writing the HDF5 file
number
167772150
Minimum interval median percentile for gatk CreateReadCountPanelOfNormals
number
5
Name for panel of normals.
string
gens
Output file format for count data
string
Options used by the cnvkit subworkflow
Path to directory for target file.
string
Options used by the mutect2 subworkflow
Name for panel of normals.
string
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.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email 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.
string
Most common options used for the pipeline
Tools to use for building Panel of Normals or models.
string
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path 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.
string
Path to a file containing ploidy priors table.
string
Path to segmental-duplication track in .bed or .bed.gz format. Overlapping intervals must be merged.
string
Path 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.
boolean
The base path to the igenomes reference files
string
s3://ngi-igenomes/igenomes/
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
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.
string