[
    {
        "id": "map_box",
        "name": "Mapping box",
        "article": "",
        "website": "",
        "git": "",
        "description": "Takes reads and fasta reference and returns a bam and stats",
        "version": "",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "map_box",
                "cname": "Map box",
                "command": null,
                "category": "mapping",
                "output_dir": "map_box",
                "inputs": [
                    {
                        "name": "reads",
                        "type": "reads"
                    },
                    {
                        "name": "fasta_ref",
                        "type": "contigs",
                        "file": "",
                        "description": "fasta reference"
                    }
                ],
                "outputs": [
                    {
                        "name": "bam",
                        "type": "bams",
                        "file": "{sample}.bam",
                        "description": "Alignment files"
                    },
                    {
                        "name": "stats",
                        "type": "txt",
                        "file": "{sample}_bamstats.txt",
                        "description": "Alignment statistics"
                    }
                ],
                "options": [
                    {
                        "name": "map_box_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "yaml": "{\n  id: map_box,\n  name: Mapping box,\n  article: \"\",\n  website: \"\",\n  git: \"\",\n  description: \"Takes reads and fasta reference and returns a bam and stats\",\n  version: \"\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: map_box,\n        cname: \"Map box\",\n        command: ,\n        category: \"mapping\",\n        output_dir: map_box,\n        inputs: [{ name: reads, type: \"reads\" },{ name: fasta_ref , type: \"contigs\", file: \"\", description: \"fasta reference\"}],\n        outputs: [\n          { name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" },\n          { name: stats, type: \"txt\", file: \"{sample}_bamstats.txt\", description: \"Alignment statistics\" }\n        ],\n        options:\n          [\n            {\n              name: map_box_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      },\n    ],\n  install:  {\n    # bwa: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/lh3\/bwa\/releases\/download\/v0.7.17\/bwa-0.7.17.tar.bz2\",\n    #   \"tar -xvjf bwa-0.7.17.tar.bz2\",\n    #   \"cd bwa-0.7.17\",\n    #   \"make -j 10\",\n    #   \"mv bwa ..\/bin\/\",\n    #   \"cd ..\",\n    #   \"rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2\"\n    # ],\n    # samtools: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n    #   \"tar -xvjf samtools-1.9.tar.bz2\",\n    #   \"cd samtools-1.9\",\n    #   \".\/configure && make\",\n    #   \"cd ..\",\n    #   \"mv samtools-1.9\/samtools bin\/samtools\",\n    #   \"rm -r samtools-1.9 samtools-1.9.tar.bz2\"\n    # ]\n  },\n}"
    }
]