nf-core/oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline
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.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringOther options specific to this pipeline.
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringWorkflow run mode.
string(?i)^(wgts|targeted|purity_estimate|panel_resource_creation|prepare_reference)$Purity estimate workflow run mode.
string(?i)^(wgts|targeted)$Type of sequencing technology.
stringName of panel to use.
stringSkip check for restricted genome.
booleanSkip check for known panels.
booleanWhich reference data types to download and extract. To be used with –mode prepare_reference.
stringManually run processes provided as a comma separated list.
stringExclude processes provided as a comma separated list.
stringInclude processes that are excluded by default, provided as a comma separated list.
stringUMI type. Sets default ‘umi settings’
stringEnable fastq-tools UMI processing.
booleanUMI delimiter fastq-tools.
stringEnable fastp UMI processing.
booleanfastp UMI location parameter (–umi_loc).
stringfastp UMI length parameter (–umi_len)
integerfastp UMI skip parameter (–umi_skip)
integer-1Enable REDUX UMI processing.
booleanUMI duplex delimiter as used by REDUX.
stringUser defined RNA read length used for Isofox.
integerUser defined Isofox expected GC ratios file.
stringUser defined Isofox expected counts files (read length dependent).
stringUser defined Isofox TPM normalisation file for panel data.
stringUser defined Isofox gene list file for panel data.
stringSemicolon-separated list of Isofox functions to run
stringTRANSCRIPT_COUNTS;ALT_SPLICE_JUNCTIONS;FUSIONS;RETAINED_INTRONSWhen positive, parallelise read alignment across multiple jobs by splitting fastq files into multiple fastq files with no more than max_fastq_records records.
integerUser defined driver gene panel used in panel resource creation, or for overriding the default file located in ref_data_hmf_data_path
stringUser defined target regions BED used in panel resource creation.
stringDuring panel resource creation, calculate copy number normalisation factors based on per-region copy number percentiles derived from the Hartwig WGS solid tumor cohort.
booleanPath to GRIDSS configuration file.
stringLog level filter for WiGiTS modules
stringCreate placeholders for reference data during stub run.
booleanReference data files and options required for the workflow.
Name of genome reference.
stringVersion of reference genome.
stringType of reference genome.
stringDo not load the iGenomes reference config.
booleantrueThe base path to the igenomes reference files
strings3://ngi-igenomes/igenomes/The URL and root path to the oncoanalyser reference files
stringThe URL and root path to the Hartwig genome reference files
stringPath to HMF data.
stringPath to panel data.
stringPath to reference genome FASTA.
stringPath to reference genome FAI.
stringPath to reference genome dict.
stringPath to reference genome bwa-mem2 index.
stringPath to reference genome img.
stringPath to reference genome GRIDSS index.
stringPath to reference genome STAR index.
stringPath to reference genome GTF.
stringbooleanParameters 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.
booleanCustom 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/oncoanalyserSuffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
stringDisplay the help message.
boolean,stringDisplay the full detailed help message.
booleanDisplay hidden parameters in the help message (only works when –help or –help_full are provided).
boolean