github.com/nf-core/rnafusion

Nextflow rnafusion analysis pipeline, part of the nf-core community.

Usage:

The typical command for running the pipeline is as follows:

nextflow run nf-core/rnafusion --reads '*_R{1,2}.fastq.gz' -profile docker

Mandatory arguments:
  --reads [file]                Path to input data (must be surrounded with quotes)
  -profile [str]                Configuration profile to use. Can use multiple (comma separated)
                                Available: docker, singularity, test, awsbatch, <institute> and more            
  --reference_path [str]        Path to reference folder (includes fasta, gtf, fusion tool ref ...)

Tool flags:
  --arriba [bool]                 Run Arriba
  --arriba_opt [str]              Specify extra parameters for Arriba
  --ericscript [bool]             Run Ericscript  
  --fusioncatcher [bool]          Run FusionCatcher
  --fusioncatcher_opt [srt]       Specify extra parameters for FusionCatcher
  --fusion_report_opt [str]       Specify extra parameters for fusion-report
  --pizzly [bool]                 Run Pizzly
  --pizzly_k [int]                Number of k-mers. Deafult 31
  --squid [bool]                  Run Squid
  --star_fusion [bool]            Run STAR-Fusion
  --star_fusion_opt [str]         Specify extra parameters for STAR-Fusion

Visualization flags:
  --arriba_vis [bool]             Generate a PDF visualization per detected fusion
  --fusion_inspector [bool]       Run Fusion-Inspector
  --fusion_inspector_opt [str]    Specify extra parameters for Fusion-Inspector

References                        If not specified in the configuration file or you wish to overwrite any of the references.
  --arriba_ref [file]             Path to Arriba reference
  --databases [path]              Database path for fusion-report
  --ericscript_ref [file]         Path to Ericscript reference
  --fasta [file]                  Path to fasta reference
  --fusioncatcher_ref [file]      Path to Fusioncatcher reference
  --gtf [file]                    Path to GTF annotation
  --star_index [file]             Path to STAR-Index reference
  --star_fusion_ref [file]        Path to STAR-Fusion reference
  --transcript [file]             Path to transcript

Options:
  --read_length [int]             Length of the reads. Default: 100
  --single_end [bool]             Specifies that the input is single-end reads

Other Options:
  --debug [bool]                  Flag to run only specific fusion tool/s and not the whole pipeline. Only works on tool flags.
  --outdir [file]                 The output directory where the results will be saved
  --email [email]                 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
  --email_on_fail [email]         Same as --email, except only send mail if the workflow is not successful
  --max_multiqc_email_size [str]  Theshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB)
  -name [str]                     Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic

AWSBatch options:
  --awsqueue [str]                The AWSBatch JobQueue that needs to be set when running on AWSBatch
  --awsregion [str]               The AWS Region for your AWS Batch job to run on
  --awscli [str]                  Path to the AWS CLI tool