{"repo":"nf-core/rnafusion","free":true,"listed":false,"github":"https://github.com/nf-core/rnafusion","clone":"git clone https://github.com/nf-core/rnafusion.git","description":"RNA-seq analysis pipeline for detection of gene-fusions","language":"Nextflow","stars":174,"topics":["nf-core","nextflow","workflow","rna-seq","rna","pipeline","fusion-genes","fusion","gene-fusion"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/rnafusion is a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from fusion callers tools (STAR-Fusion, arriba and FusionCatcher) are created, and are also aggregated, most notably in a pdf visualisation document, a vcf data collection file, and html and tsv reports. In parallel StringTie and CTAT-Splicing collect additional information on splicing events. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website. In rnafusion the full-sized test includes reference building and fusion detection. The test dataset is taken from here. Pipeline summary References The references for the pipeline can be downloaded from the nf-core AWS megatests S3 bucket using the following command for the AWS CLI tool: The path to the downloaded references can then be provided to the pipeline with the --genomes base parameter. ⚠️ Please note that the references are large and can take a long time to download, so it is recommended to download them once and use them for all future runs of the pipeli","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/rnafusion/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}