nf-core-sarek.json

{
    "name": "nf-core-sarek",
    "description": "Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.\n\nIt's built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.",
    "homepage": "https://nf-co.re/sarek",
    "biotoolsID": "nf-core-sarek",    
    "version": [
        "2.0.0",
        "2.1.0",
        "2.2.0",
        "2.2.1",
        "2.2.2",
        "2.3",
        "2.3.FIX1",
        "2.5",
        "2.5.1",
        "2.5.2",
        "2.6",
        "2.6.1"
    ],    
    "relation": [
        {
            "biotoolsID": "caw",
            "type": "isNewVersionOf"
        },
        {
        "type": "isNewVersionOf",
        "biotoolsID": "sarek"
        }
    ],
    "function": [
        {
            "operation": [
                {
                    "uri": "http://edamontology.org/operation_3731",
                    "term": "Sample comparison"
                },
                {
                    "uri": "http://edamontology.org/operation_0361",
                    "term": "Sequence annotation"
                },
                {
                    "uri": "http://edamontology.org/operation_3227",
                    "term": "Variant calling"
                }
            ],
            "input": [
                {
                    "data": {
                        "uri": "http://edamontology.org/data_3497",
                        "term": "DNA sequence (raw)"
                    },
                    "format": [
                        {
                            "uri": "http://edamontology.org/format_1930",
                            "term": "FASTQ"
                        }
                    ]
                },
                {
                    "data": {
                        "uri": "http://edamontology.org/data_3494",
                        "term": "DNA sequence"
                    },
                    "format": [
                        {
                            "uri": "http://edamontology.org/format_2572",
                            "term": "BAM"
                        }
                    ]
                }
            ],
            "output": [
                {
                    "data": {
                        "uri": "http://edamontology.org/data_3498",
                        "term": "Sequence variations"
                    },
                    "format": [
                        {
                            "uri": "http://edamontology.org/format_3016",
                            "term": "VCF"
                        }
                    ]
                }
            ]
        }
    ],
    "toolType": [
        "Command-line tool",
        "Workflow"
    ],
    "topic": [
        {
            "uri": "http://edamontology.org/topic_2640",
            "term": "Oncology"
        },
        {
            "uri": "http://edamontology.org/topic_0622",
            "term": "Genomics"
        },
        {
            "uri": "http://edamontology.org/topic_3673",
            "term": "Whole genome sequencing"
        },
        {
            "uri": "http://edamontology.org/topic_0769",
            "term": "Workflows"
        }
    ],
    "operatingSystem": [
        "Linux"
    ],
    "language": [
        "Groovy"
    ],
    "license": "MIT",
    "collectionID": [
        "nf-core"
    ],
    "maturity": "Mature",    
    "accessibility": "Open access",
    "link": [
        {
            "url": "https://github.com/nf-core/sarek",
            "type": [
                "Repository"
            ],
            "note": "Github Repository"
        },
        {
            "url": "https://nfcore.slack.com/channels/sarek",
            "type": [
                "Social media"
            ],
            "note": "Slack channel"
        }
    ],
    "download": [
        {
            "url": "https://github.com/nf-core/sarek/releases/tag/2.6.1",
            "type": "Source code",
            "note": "Release 2.6.1",
            "version": "2.6.1"
        }
    ],
    "documentation": [
        {
            "url": "https://nf-co.re/sarek",
            "type": [
                "General"
            ] 
        },
        {
            "url": "https://nf-co.re/sarek/usage",
            "type": [
                "User manual"
            ]
        },
        {
            "url": "https://nf-co.re/usage/installation",
            "type": [
                "Installation instructions"
            ]            
        },
        {
            "url": "https://github.com/nf-core/sarek/blob/master/LICENSE",
            "type": [
                "Terms of use"
            ]            
        }
    ],
    "publication": [        
        {
            "doi": "10.12688/f1000research.16665.1",
            "pmid": "32269765",
            "pmcid": "PMC7111497",
            "type": [
                "Primary"
            ]            
        },
        {
            "doi": "10.1101/316976",
            "type": [
                "Other"
            ],            
            "note": "F1000 article preprint on BioRxiv"            
        },
        {
            "doi": "10.1038/s41587-020-0439-x",
            "pmid": "32055031",            
            "type": [
                "Other"
            ],
            "note": "This is the publication about the nf-core framework"
        }
    ],
    "credit": [
        {
            "name": "Maxime U. Garcia",
            "email": "maxime.garcia@scilifelab.se",
            "url": "https://maxulysse.github.io/",
            "orcidid": "https://orcid.org/0000-0003-2827-9261",
            "typeEntity": "Person",
            "typeRole": [
                "Primary contact",
                "Developer",
                "Maintainer"
            ]
        },
        {
            "name": "Szilvester Juhos",
            "email": "szilveszter.juhos@scilifelab.se",
            "typeEntity": "Person",
            "typeRole": [
                "Primary contact",
                "Developer",
                "Maintainer"
            ]
        },
        {
            "name": "Science for Life Laboratory - SciLifeLab",
            "url": "https://www.scilifelab.se/",
            "typeEntity": "Institute"
        },
        {
            "name": "National Genomics Infrastructure - NGI",
            "url": "https://ngisweden.scilifelab.se/",
            "typeEntity": "Division"
        },
        {
            "name": "National Bioinformatics Infrastructure Sweden - NBIS",
            "url": "https://nbis.se/",
            "typeEntity": "Division"
        },
        {
            "name": "Barntumörbanken",
            "url": "https://ki.se/forskning/barntumorbanken",
            "typeEntity": "Institute"
        },
        {
            "name": "Quantitative Biology Center - QBiC",            
            "url": "https://www.qbic.uni-tuebingen.de/",
            "typeEntity": "Institute"
        },
        {
            "name": "nf-core",
            "url": "https://nf-co.re",
            "typeEntity": "Consortium"                      
        }
    ],    
    "owner": "nf-core",    
    "editPermission": {
        "type": "group",
        "authors": [
            "MaxUlysse",
            "malinlarsson",
            "szilva",
            "fhanssen",
            "JoseEspinosa",
            "ewels",
            "nf-core"           
        ]
    },
    "validated": 0,
    "homepage_status": 0,
    "elixir_badge": 0    
}