[
    {
        "id": "jellyfish_count",
        "name": "JELLYFISH count",
        "article": "10.1093\/bioinformatics\/btr011",
        "website": "http:\/\/www.genome.umd.edu\/jellyfish.html",
        "git": "https:\/\/github.com\/gmarcais\/Jellyfish",
        "description": "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence",
        "version": "2.3.0",
        "documentation": "http:\/\/www.genome.umd.edu\/docs\/JellyfishUserGuide.pdf",
        "multiqc": "jellyfish",
        "commands": [
            {
                "name": "jellyfish_count",
                "cname": "Jellyfish count",
                "command": "jellyfish count",
                "category": "quantification",
                "output_dir": "jellyfish",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "kmer_counts",
                        "type": "jellyfishcounts",
                        "file": "counts.jf",
                        "description": "Jellyfish kmer counts file"
                    }
                ],
                "options": [
                    {
                        "name": "jellyfish_count_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "jellyfish_count_canonical_kmer",
                        "prefix": null,
                        "type": "checkbox",
                        "value": true,
                        "label": "-C : Save in the hash only canonical k-mers, while the count is the number of occurrences of both a k-mer and it reverse complement"
                    },
                    {
                        "name": "jellyfish_count_kmer_len",
                        "prefix": "-m",
                        "type": "numeric",
                        "value": 21,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "K-mers length"
                    },
                    {
                        "name": "jellyfish_count_hash_size",
                        "prefix": "-s",
                        "type": "numeric",
                        "value": 100000000,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Kmer size estimation"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "jellyfish": [
                "Guillaume Mar\u00e7ais, Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, Volume 27, Issue 6, 15 March 2011, Pages 764-770, https:\/\/doi.org\/10.1093\/bioinformatics\/btr011"
            ]
        },
        "yaml": "{\n  id: jellyfish_count,\n  name: JELLYFISH count,\n  article: \"10.1093\/bioinformatics\/btr011\",\n  website: \"http:\/\/www.genome.umd.edu\/jellyfish.html\",\n  git: \"https:\/\/github.com\/gmarcais\/Jellyfish\",\n  description: \"Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence\",\n  version: \"2.3.0\",\n  documentation: \"http:\/\/www.genome.umd.edu\/docs\/JellyfishUserGuide.pdf\",\n  multiqc: \"jellyfish\",\n  commands:\n    [\n      {\n        name: jellyfish_count,\n        cname: \"Jellyfish count\",\n        command: jellyfish count,\n        category: \"quantification\",\n        output_dir: jellyfish,\n        inputs: [{ name: read, type: \"reads\" }],\n        outputs: [{ name: kmer_counts, type: \"jellyfishcounts\", file: counts.jf, description: \"Jellyfish kmer counts file\" }],\n        options:\n          [\n            {\n              name: jellyfish_count_threads,\n              prefix: -t,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use\",\n            },\n            {\n              name: jellyfish_count_canonical_kmer,\n              prefix: ,\n              type: checkbox,\n              value: TRUE,\n              label: \"-C : Save in the hash only canonical k-mers, while the count is the number of occurrences of both a k-mer and it reverse complement\",\n            },\n            {\n              name: jellyfish_count_kmer_len,\n              prefix: -m,\n              type: numeric,\n              value: 21,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"K-mers length\",\n            },\n            {\n              name: jellyfish_count_hash_size,\n              prefix: -s,\n              type: numeric,\n              value: 100000000,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Kmer size estimation\",\n            },\n          ]\n      },\n    ],\n  install:  {\n    # jellyfish: [\n    #   \"cd \/opt\/biotools\/bin\",\n    #   \"wget -O jellyfish https:\/\/github.com\/gmarcais\/Jellyfish\/releases\/download\/v2.3.0\/jellyfish-linux\",\n    #   \"chmod +x \/opt\/biotools\/bin\/jellyfish\"\n    # ],\n  },\n  citations:  {\n    jellyfish: [\n      \"Guillaume Mar\u00e7ais, Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, Volume 27, Issue 6, 15 March 2011, Pages 764-770, https:\/\/doi.org\/10.1093\/bioinformatics\/btr011\"\n    ]\n  }\n}"
    }
]