[
    {
        "id": "velvet",
        "name": "Velvet",
        "description": "Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.",
        "version": "1.2.10",
        "website": "https:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/",
        "git": "https:\/\/github.com\/dzerbino\/velvet\/tree\/master",
        "documentation": "https:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/Manual.pdf",
        "article": "10.1101\/gr.074492.107",
        "multiqc": "custom",
        "commands": [
            {
                "name": "velvet",
                "cname": "Velvet",
                "command": "velvet",
                "category": "assembly",
                "output_dir": "velvet",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "contigs",
                        "type": "fasta",
                        "file": "{sample}_contigs.fa",
                        "description": "fasta file of contigs longer than twice hash length"
                    },
                    {
                        "name": "stats",
                        "type": "txt",
                        "file": "{sample}_stats.txt",
                        "description": "stats file (tab-spaced) useful for determining appropriate coverage cutoff"
                    },
                    {
                        "name": "LastGraph",
                        "type": "LastGraph",
                        "file": "{sample}_LastGraph",
                        "description": "special formatted file with all the information on the final graph"
                    }
                ],
                "options": [
                    {
                        "name": "velvet_hash_length",
                        "prefix": "-min_contig_lgth",
                        "type": "text",
                        "value": "31",
                        "label": "hash_length : EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be reduced) OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 31 (if above, will be reduced) and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s"
                    },
                    {
                        "name": "velvet_min_contig_lgth",
                        "prefix": "-min_contig_lgth",
                        "type": "numeric",
                        "value": "NA",
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "-min_contig_lgth : minimum contig length exported to contigs.fa file (default: hash length * 2)"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "velvet": [
                "Zerbino, D. R., & Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research, 18(5), 821-829"
            ]
        },
        "yaml": "{\n  id: velvet,\n  name: Velvet,\n  description: \"Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.\",\n  version: \"1.2.10\",\n  website: \"https:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/\",\n  git: \"https:\/\/github.com\/dzerbino\/velvet\/tree\/master\",\n  documentation: \"https:\/\/www.ebi.ac.uk\/~zerbino\/velvet\/Manual.pdf\",\n  article: 10.1101\/gr.074492.107 ,\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: velvet,\n        cname: \"Velvet\",\n        command: velvet,\n        category: \"assembly\",\n        output_dir: velvet,\n        inputs: [{ name: read, type: \"reads\" }],\n        outputs: [\n          { name: contigs, type: \"fasta\", file: \"{sample}_contigs.fa\", description: \"fasta file of contigs longer than twice hash length\" },\n          { name: stats, type: \"txt\", file: \"{sample}_stats.txt\", description: \"stats file (tab-spaced) useful for determining appropriate coverage cutoff\" },\n          { name: LastGraph, type: \"LastGraph\", file: \"{sample}_LastGraph\", description: \"special formatted file with all the information on the final graph\" },\n          #{ name: , file: \"{sample}_velvet_asm.afg\", description: \"(if requested) AMOS compatible assembly file\" },\n        ],\n        options:\n          [\n            {\n              name: velvet_hash_length,\n              prefix: -min_contig_lgth,\n              type: text,\n              value: \"31\",\n              label: \"hash_length : EITHER an odd integer (if even, it will be decremented) <= 31 (if above, will be reduced) OR: m,M,s where m and M are odd integers (if not, they will be decremented) with m < M <= 31 (if above, will be reduced) and s is a step (even number). Velvet will then hash from k=m to k=M with a step of s\",\n            },\n            {\n              name: velvet_min_contig_lgth,\n              prefix: -min_contig_lgth,\n              type: numeric,\n              value: \"NA\",\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"-min_contig_lgth : minimum contig length exported to contigs.fa file (default: hash length * 2)\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # velvet: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget -O velvet-1.2.10.tar.gz https:\/\/github.com\/dzerbino\/velvet\/archive\/v1.2.10.tar.gz\",\n    #   \"tar -xvzf velvet-1.2.10.tar.gz\",\n    #   \"cd velvet-1.2.10\",\n    #   \"make -j 10\",\n    #   \"mv velvet* ..\/bin\",\n    #   \"cd ..\",\n    #   \"rm -r velvet-1.2.10 velvet-1.2.10.tar.gz\"\n    # ]\n  },\n  citations:  {\n    velvet: [\n      \"Zerbino, D. R., & Birney, E. (2008). Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome research, 18(5), 821-829\"\n    ],\n  }\n}\n"
    }
]