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, 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