nf-core/rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
2.0.0). 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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
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
stringPath to fusioncatcher references
stringFeed filtered fusionreport fusions to fusioninspector
booleanBuild 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
stringReference genome related files and options required for the workflow.
Name of iGenomes reference.
stringIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.
See the nf-core website docs for more details.
Path to FASTA genome file.
string^\S+\.fn?a(sta)?(\.gz)?$This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.
Path to GTF genome file.
string^\S+\.gtf?(\.gz)?$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?$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$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|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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$Do not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${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
booleanThis will reported in the BAM header as CN
Sequencing platform
booleanThis 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