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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringOther options specific to this pipeline.
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Workflow run mode.
string^(wgts|targeted|purity_estimate|panel_resource_creation|prepare_reference)Purity estimate workflow run mode.
string^(wgts|targeted)Name of panel to use.
stringSkip check for restricted genome.
booleanSkip check for known panels.
booleanManually 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.
stringWhich reference data types to download and extract.
stringCreate placeholders for reference data during stub run.
booleanWhen positive, will use fastp to split fastq files so that each resultant fastq file has no more than max_fastq_records records. When nonpositive, fastp is not used and the provided fastq files are passed as-is to the aligner.
integer10000000Enable 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.
stringPath to GRIDSS configuration file.
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_INTRONSUser 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.
stringLog level filter for WiGiTS modules
stringReference 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 base path to the HMF genome reference files
stringhttps://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomesPath 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.
stringPath to HLA slice BED file.
string^\S+\.bed$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
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.
string