{"repo":"nf-core/viralintegration","free":true,"listed":false,"github":"https://github.com/nf-core/viralintegration","clone":"git clone https://github.com/nf-core/viralintegration.git","description":"Analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach.","language":"Python","stars":18,"topics":["nextflow","nf-core","pipeline","workflow","chimeric-alignment","ctat","virus","viral-integration","virusintegrationfinder"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/viralintegration is a bioinformatics best-practice analysis pipeline for the identification of viral integration events in genomes using a chimeric read approach. It was initially based on the CTAT-VirusIntegrationFinder. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! 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. Pipeline summary 1. Input Check - Input path to sample FASTAs in samplesheet.csv - Check that sample meets requirements (samplesheet check) 2. Read QC ( FastQC ) 3. Align reads to human genome - Generate index and perform alignment (","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/viralintegration/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."}