nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
2.1.0). The latest
stable release is
4.0.0
.
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 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
stringBuild 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
stringCOSMIC username
stringCOSMIC password
stringOptions to adjust read trimming criteria.
Preform trimming of reads, default: false
booleanReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringPath to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$Path to GTF genome file.
string^\S+\.gtf?(\.gz)?$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?$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|day)\s*)+$Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanRun this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.
booleanUse to pull docker containers to run with singularity
booleanSequencing center
stringSequencing platform
stringWhether to ignore the GTF in STAR alignment
boolean