nf-core/oncoanalyser
A comprehensive cancer DNA/RNA analysis and reporting pipeline
1.0.0). The latest
stable release is
2.1.0
.
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)Name of panel to use.
stringSkip check for restricted genome.
booleanRun only processes manually provided in processes_include.
booleanPipeline processes to exclude.
stringPipeline processes to include.
stringPrepare and write reference output only.
booleanCreate 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.
integerPath 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_INTRONSReference 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.
booleanPath to HMF data.
stringPath to panel data.
stringPath to VIRUSBreakend database (directory or tarball).
stringPath to HLA slice BED file.
^\S+\.bed$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleantrueShow all params when using --help
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
boolean