[
    {
        "id": "samtools_stats",
        "name": "SAM tools stats",
        "article": "10.1093\/bioinformatics\/btp352",
        "website": "http:\/\/samtools.sourceforge.net\/",
        "git": "https:\/\/github.com\/samtools\/samtools",
        "description": "The program collects statistics from BAM files",
        "version": "1.17",
        "documentation": "http:\/\/www.htslib.org\/doc\/samtools.html",
        "multiqc": "samtools",
        "commands": [
            {
                "name": "samtools_stats",
                "command": "samtools stats",
                "category": "quality",
                "output_dir": "samtools_stats",
                "inputs": [
                    {
                        "name": "bam",
                        "type": "bams"
                    }
                ],
                "outputs": [
                    {
                        "name": "stats",
                        "type": "txt",
                        "file": "{sample}_samtools_stats.txt",
                        "description": "samtools stats command output"
                    }
                ],
                "options": [
                    {
                        "name": "samtools_stats_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "samtools": [
                "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352"
            ]
        },
        "yaml": "{\n  id: samtools_stats,\n  name: SAM tools stats,\n  article: 10.1093\/bioinformatics\/btp352,\n  website: \"http:\/\/samtools.sourceforge.net\/\",\n  git: \"https:\/\/github.com\/samtools\/samtools\",\n  description: \"The program collects statistics from BAM files\",\n  version: \"1.17\",\n  documentation: \"http:\/\/www.htslib.org\/doc\/samtools.html\",\n  multiqc: \"samtools\",\n  commands:\n    [\n      {\n        name: samtools_stats,\n\n        command: samtools stats,\n        category: \"quality\",\n        output_dir: samtools_stats,\n        inputs: [{ name: bam, type: \"bams\" }],\n        outputs:\n          [\n            { name: stats, type: \"txt\", file: \"{sample}_samtools_stats.txt\", description: \"samtools stats command output\" }\n          ],\n        options:\n          [\n            {\n              name: samtools_stats_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    # 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  citations:  {\n    samtools: [\n      \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n    ]\n  }\n}\n"
    }
]