nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
2.3.0
). The latest
stable release is
3.0.2
.
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$
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})$
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
Path to reference folder
string
ensembl version
integer
105
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
Feed filtered fusionreport fusions to fusioninspector
boolean
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
Display fusions identified with 2 tools or more
boolean
true
Build or run pizzly references/analyses
boolean
Path to pizzly output
string
Path to pizzly references
string
Build or run squid references/analyses
boolean
Path to squid output
string
Path to squid references
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
Path to fusions to add to the input of fusioninspector
string
COSMIC username
string
COSMIC password
string
Use QIAGEN instead of SANGER to download COSMIC database
boolean
Options to adjust read trimming criteria.
Preform trimming of reads, default: false
boolean
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, squid, 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
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
Maximum amount of memory that can be requested for any single job.
string
128.GB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Maximum amount of time that can be requested for any single job.
string
240.h
^(\d+\.?\s*(s|m|h|day)\s*)+$
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
Email 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.
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
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
Directory to keep pipeline Nextflow logs and reports.
string
${params.outdir}/pipeline_info
Boolean whether to validate parameters against the schema at runtime
boolean
true
Show all params when using --help
boolean
Sequencing center
string
Sequencing platform
string
Whether to ignore the GTF in STAR alignment
boolean