nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
Skip analysis steps
Skip QC steps
boolean
Skip visualisation steps
boolean
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.
string
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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Specifies which analysis type for the pipeline - either build references or analyse data
boolean
COSMIC username
string
COSMIC password
string
Path to reference folder
string
ensembl version
integer
102
If set, starfusion references are built from scratch instead of downloaded (default)
boolean
Read length
integer
100
Build or run all references/analyses
boolean
Build or run arriba references/analyses
boolean
Path to arriba references
string
Path to arriba reference blacklist
string
Path to arriba reference cytobands
string
Path to arriba reference known fusions
string
Path to arriba reference protein domain
string
Path to arriba output
string
Path to ensembl references
string
Build or run fusioncatcher references/analyses
boolean
Path to fusioncatcher output
string
Use limitSjdbInsertNsj with int for fusioncatcher
integer
Path to fusioncatcher references
string
Use limitSjdbInsertNsj with int for fusioninspector STAR process
integer
Skip fusion-report. --fusioninspector_fusions PATH needed to provide a fusion list as input
boolean
Path to a fusion list file built with format GENE1--GENE2
string
Build fusionreport references
boolean
Path to fusionreport references
string
Path to HGNC database file
string
Path to HGNC timestamp file for database retrieval
string
Use QIAGEN instead of SANGER to download COSMIC database
boolean
Path to salmon index
string
Build or run starfusion references/analyses
boolean
Path to starfusion output
string
Path to starfusion references
string
Build or run starindex references/analyses
boolean
Path to starindex references
string
Run stringtie analysis
boolean
Discard fusions identified by less than INT tools
integer
Path to fusions to add to the input of fusioninspector
string
Options to adjust read trimming criteria.
Preform fastp trimming of reads, default: false
boolean
Preform tail trimming of reads, default: null
integer
Path to adapter fasta file: default: []
string
Option 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
string
Reference genome related files and options required for the workflow.
Name of iGenomes reference.
string
Path 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.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
If 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.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer
16
Use 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.
string
128.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.
string
240.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.
boolean
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
The 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
By 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.
boolean
By default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
boolean
Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/
Sequencing center
string
This will reported in the BAM header as CN
Sequencing platform
string
This will reported in the BAM header as PL.
Whether to ignore the GTF in STAR alignment
boolean
Setting false will use GTF file for STAR alignment