nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
Skip analysis steps
Skip QC steps
booleanSkip visualisation steps
booleanDefine 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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringSpecifies which analysis type for the pipeline - either build references or analyse data
booleanCOSMIC username
stringCOSMIC password
stringPath to reference folder
stringensembl version
integer102If set, starfusion references are built from scratch instead of downloaded (default)
booleanRead length
integer100Build or run all references/analyses
booleanBuild or run arriba references/analyses
booleanPath to arriba references
stringPath to arriba reference blacklist
stringPath to arriba reference cytobands
stringPath to arriba reference known fusions
stringPath to arriba reference protein domain
stringPath to arriba output
stringPath to ensembl references
stringBuild or run fusioncatcher references/analyses
booleanPath to fusioncatcher output
stringUse limitSjdbInsertNsj with int for fusioncatcher
integerPath to fusioncatcher references
stringUse limitSjdbInsertNsj with int for fusioninspector STAR process
integerSkip fusion-report. --fusioninspector_fusions PATH needed to provide a fusion list as input
booleanPath to a fusion list file built with format GENE1--GENE2
stringBuild fusionreport references
booleanPath to fusionreport references
stringPath to HGNC database file
stringPath to HGNC timestamp file for database retrieval
stringUse QIAGEN instead of SANGER to download COSMIC database
booleanBuild or run starfusion references/analyses
booleanPath to starfusion output
stringPath to starfusion references
stringBuild or run starindex references/analyses
booleanPath to starindex references
stringRun stringtie analysis
booleanDiscard fusions identified by less than INT tools
integerPath to fusions to add to the input of fusioninspector
stringOptions to adjust read trimming criteria.
Preform fastp trimming of reads, default: false
booleanPreform tail trimming of reads, default: null
integerPath to adapter fasta file: default: []
stringOption to compress BAM files to CRAM.
List of tools for which to compress BAM file to CRAM,default: [], options: arriba, starfusion. Leave no space between options
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to FASTA genome index file.
string^\S+\.fn?ai(\.gz)?$Path to GTF genome file.
string^\S+\.gtf?(\.gz)?$Path to GTF genome file.
string^\S+\.gtf?(\.gz)?$Path to GTF genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF genome file.
string^\S+\.refflat?$Path to ribosomal interval list.
string^\S+\.interval_list?$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
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
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.
Sequencing center
stringThis will reported in the BAM header as CN
Sequencing platform
stringThis will reported in the BAM header as PL.
Whether to ignore the GTF in STAR alignment
booleanSetting false will use GTF file for STAR alignment