nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
2.4.0). The latest
stable release is
3.0.2
.
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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleanPath to reference folder
stringensembl version
integer105If 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
stringFeed filtered fusionreport fusions to fusioninspector
booleanUse 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
stringDisplay fusions identified with 2 tools or more
booleantrueBuild or run pizzly references/analyses
booleanPath to pizzly output
stringPath to pizzly references
stringBuild or run squid references/analyses
booleanPath to squid output
stringPath to squid references
stringBuild 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
booleanPath to fusions to add to the input of fusioninspector
stringCOSMIC username
stringCOSMIC password
stringUse QIAGEN instead of SANGER to download COSMIC database
booleanOptions to adjust read trimming criteria.
Preform trimming of reads, default: false
booleanPreform 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, squid, 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?$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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.
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
stringCustom 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
booleanValidation of parameters fails when an unrecognised parameter is found.
booleanValidation of parameters in lenient more.
booleanSequencing center
stringSequencing platform
stringWhether to ignore the GTF in STAR alignment
boolean