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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringOther options specific to this pipeline.
Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
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.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe c lashes between custom parameters and those supplied in igenomes.config.
Path to HMF data.
stringPath to panel data.
stringPath to VIRUSBreakend database (directory or tarball).
stringPath to HLA slice BED file.
undefined^\S+\.bed$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Boolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.