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.
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.
stringgermlinecnvcallerOutput 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's IntervalListTools.
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.
Maximum chunk size when writing the HDF5 file
number167772150Minimum interval median percentile for gatk CreateReadCountPanelOfNormals
number5Genomic intervals with a median (across samples) of fractional coverage (optionally corrected for GC bias) less than or equal to this percentile are filtered out. (This is the first filter applied.)
Name for panel of normals.
stringgensOutput file format for count data
stringOptions used by the cnvkit subworkflow
Path to directory for target file.
stringSpecify the path to the target file for CNVkit.
Options 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.
A 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})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringMost common options used for the pipeline
Tools to use for building Panel of Normals or models.
string^((cnvkit|germlinecnvcaller|gens|mutect2)?,?)*(?<!,)$Multiple tools separated with commas.
Tools available: CNVKIT,germlinecnvcaller,gens,mutect2
Reference 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)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to sequence dictionary file
string^\S+\.dict$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$If the regions you would like to exclude are in bed format, use this option. If you have an interval_list file, use exclude_interval_list parameter instead.
Path to directory for exclude_interval_list file.
string^\S+\.interval_list$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.
Path to a file containing ploidy priors table.
stringUsed by GATK's DeterminGermlineContigPloidy.
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.
Path to target bed file
string^\S+\.bed$Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
The base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
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