{"id":38724745,"url":"https://github.com/rki-mf1/cievad","last_synced_at":"2026-01-17T11:14:36.678Z","repository":{"id":241562014,"uuid":"638524697","full_name":"rki-mf1/cievad","owner":"rki-mf1","description":"A tool suite for a simple, streamlined and rapid evaluation of variant callsets","archived":false,"fork":false,"pushed_at":"2024-09-16T14:35:27.000Z","size":48341,"stargazers_count":3,"open_issues_count":7,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-09-16T16:42:37.485Z","etag":null,"topics":["benchmarking","bioinformatics","genomics","indels","nextflow","ngs","oxford-nanopore","snps","variant-calling"],"latest_commit_sha":null,"homepage":"https://github.com/rki-mf1/cievad","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rki-mf1.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-05-09T14:35:43.000Z","updated_at":"2024-09-16T14:35:33.000Z","dependencies_parsed_at":"2024-08-26T14:39:54.834Z","dependency_job_id":null,"html_url":"https://github.com/rki-mf1/cievad","commit_stats":null,"previous_names":["rki-mf1/cievad"],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/rki-mf1/cievad","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rki-mf1%2Fcievad","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rki-mf1%2Fcievad/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rki-mf1%2Fcievad/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rki-mf1%2Fcievad/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rki-mf1","download_url":"https://codeload.github.com/rki-mf1/cievad/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rki-mf1%2Fcievad/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28506694,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-17T10:25:30.148Z","status":"ssl_error","status_checked_at":"2026-01-17T10:25:29.718Z","response_time":85,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["benchmarking","bioinformatics","genomics","indels","nextflow","ngs","oxford-nanopore","snps","variant-calling"],"created_at":"2026-01-17T11:14:36.610Z","updated_at":"2026-01-17T11:14:36.670Z","avatar_url":"https://github.com/rki-mf1.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![run with conda](https://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000\u0026logo=anaconda)](https://docs.conda.io/en/latest/)\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A520.04.0-23aa62.svg)](https://www.nextflow.io/)\n![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/rki-mf1/cievad/test_basics.yml?logo=github\u0026label=tests)\n![GitHub Release](https://img.shields.io/github/v/release/rki-mf1/cievad?logo=github)\n![GitHub commit activity](https://img.shields.io/github/commit-activity/y/rki-mf1/cievad)\n\n# CIEVaD\n\u003cins\u003eC\u003c/ins\u003eontinuous \u003cins\u003eI\u003c/ins\u003entegration and \u003cins\u003eE\u003c/ins\u003evaluation for \u003cins\u003eVa\u003c/ins\u003eriant \u003cins\u003eD\u003c/ins\u003eetection. This repository provides a tool suite for simple, streamlined and rapid creation and evaluation of genomic variant callsets. It is primarily designed for continuous integration of variant detection software and a plain containment check between sets of variants. The tools suite utilizes the _conda_ package management system and _nextflow_ workflow language.\n\n## Contents:\n1. [System requirements](#system-requirements)\n2. [Installation](#installation)\n3. [Usage](#usage)\n4. [Help](#help)\n5. [Citation](#citation)\n\n\n## System requirements:\n\nThis tool suite was developed for Linux and is the only officially supported operating system here.\nHaving any derivative of the conda package management system installed is the only strict system requirement.\nA recent version (≥20.04.0) of nextflow is required to execute the workflows, but can easily be installed via conda.\nFor an installation instruction of nextflow via conda see [Installation](#installation).\n\n\u003cdetails\u003e\u003csummary\u003e🖥️ See list of tested setups: \u003c/summary\u003e\n   \n| Requirement | Tested with |\n| --- | --- |\n| 64 bits Linux operating system | Ubuntu 20.04.5 LTS |\n| [Conda](https://docs.conda.io/en/latest/) | vers. 23.5.0, 24.1.2|\n| [Nextflow](https://nextflow.io/) | vers. 20.04.0, 23.10.1 |\n\n\u003c/details\u003e\n\n\n## Installation:\n\n1. Download the repository:\n```\ngit clone https://github.com/rki-mf1/cievad.git\n```\n\n2. [Optional] Install nextflow if not yet on your system. For good practise you should use a new conda environment:\n```\nconda deactivate\nconda create -n cievad -c bioconda nextflow\nconda activate cievad\n```\n\n\n## Usage:\n\nThis tool suite provides multiple functional features to generate synthetic sequencing data, generate sets of ground truth variants (truthsets) and evaluate sets of predicted variants (callsets).\nThere are two main workflows, `hap.nf` and `eval.nf`. \nBoth workflows are executed via the nextflow command line interface (CLI).\n\u003cdetails\u003e\u003csummary\u003e⚠️ Run commands from the root directory: \u003c/summary\u003e\nWithout further ado, please run the commands from a terminal at the top folder (root directory) of this repository.\nOtherwise relative paths within the workflows might be invalid.\n\u003c/details\u003e\n\n### Generating haplotype data\nThe minimal command to generate haplotype data is\n```\nnextflow run hap.nf -profile local,conda\n```\n\nThis generates the following data within the `\u003cproject_root\u003e/results/` directory:\n- a haplotype (FASTA), which is a copy of the provided reference sequence but deviates by a set of synthetic genomic variants\n- the variant set (VCF) of synthetic genomic variants in the haplotype\n- a set of reads (FASTQ) representing a sequencing experiment from the haplotype\n\n### Evaluating variant calls\nThe minimal command to evaluate the accordance between a truthset (generated data) and a callset is\n```\nnextflow run eval.nf -profile local,conda --callsets_dir \u003cpath/to/callsets\u003e\n```\nwhere `--callsets_dir` is the parameter to specify a folder containing the callset VCF files.\nCurrently, a callset within this folder has to follow the naming convention `callset_\u003cX\u003e.vcf[.gz]` where _\\\u003cX\\\u003e_ is the integer of the corresponding truthset.\nAlternatively, one can provide a sample sheet of comma separated values (CSV file) with the columns \"index\", \"truthset\" and callset\", where \"index\" is an integer from 1 to n (number of samples) and \"callset\"/\"truthset\" are paths to the pairwise matching VCF files.\nCallsets can optionally be _gzip_ compressed.\nThe command for the sample sheet input is\n```\nnextflow run eval.nf -profile local,conda --sample_sheet \u003cpath/to/sample_sheet\u003e\n```\n\nThis generates the following data within the `\u003cproject_root\u003e/results/` directory:\n- a report (CSV, JSON) about accordance between the synthetic variant set and a given corresponding callset\n- a report (CSV) with statistis across all tested individuals\n\n### Tuning the workflow parameters\nCIEVaD enables access and finetuning to a vast majority of parameters of the internal software tools.\nThe parameters to adjust the workflows are listed on their respective help pages.\nTo inspect the help pages type `--help` after the script name, e.g. `nextflow run hap.nf --help` for the hap.nf workflow.\nParameters can be adjusted via the CLI or directly within the _nextflow.config_ file.\nMind that parameters provided by the CLI will overwrite parameters set in config.\nMore information about tuning crucial parameters, e.g. [read quality](https://github.com/rki-mf1/cievad/wiki/Parameterization-of-the-workflow) and [genome coverage](https://github.com/rki-mf1/cievad/wiki/FAQ---Troubleshooting), can be found in the Wiki.\n\n## Help:\n\nVisit the project [wiki](https://github.com/rki-mf1/cievad/wiki) for more detail information on parameters, help and FAQs. \u003cbr\u003e\nPlease file issues, bug reports and questions to the [issues](https://github.com/rki-mf1/cievad/issues) section.\n\n## Citation:\n\nWe have a [manuscript](https://www.mdpi.com/1999-4915/16/9/1444) available for CIEVaD.\nIf you use CIEVaD please cite\n```\n@article{krannich2024cievad,\n  title={CIEVaD: A Lightweight Workflow Collection for the Rapid and On-Demand Deployment of End-to-End Testing for Genomic Variant Detection},\n  author={Krannich, Thomas and Ternovoj, Dmitrii and Paraskevopoulou, Sofia and Fuchs, Stephan},\n  journal={Viruses},\n  volume={16},\n  number={9},\n  pages={1444},\n  year={2024},\n  doi={10.3390/v16091444}\n}\n```\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frki-mf1%2Fcievad","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frki-mf1%2Fcievad","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frki-mf1%2Fcievad/lists"}