[
    {
        "id": "bowtie2",
        "name": "Bowtie2",
        "article": "10.1038\/nmeth.1923",
        "website": "http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/index.shtml",
        "git": "https:\/\/github.com\/BenLangmead\/bowtie2",
        "description": "A fast and sensitive gapped read aligner",
        "version": "2.5.1",
        "documentation": "http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/manual.shtml",
        "multiqc": "bowtie2",
        "commands": [
            {
                "name": "bowtie2_PE",
                "cname": "Bowtie2 PE",
                "command": "bowtie2",
                "category": "mapping",
                "output_dir": "bowtie2\/PE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    },
                    {
                        "name": "index",
                        "type": "bowtie2_index",
                        "file": "index",
                        "description": "Index files for bowtie2 alignment"
                    }
                ],
                "outputs": [
                    {
                        "name": "bam",
                        "type": "bams",
                        "file": "{sample}.bam",
                        "description": "Alignment files"
                    }
                ],
                "options": [
                    {
                        "name": "bowtie2_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use to align reads"
                    },
                    {
                        "name": "bowtie2_minins_PE",
                        "prefix": "-I",
                        "type": "numeric",
                        "value": 0,
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "The minimum insert size for valid paired-end alignments"
                    },
                    {
                        "name": "bowtie2_maxins_PE",
                        "prefix": "-X",
                        "type": "numeric",
                        "value": 250,
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "The maximum insert size for valid paired-end alignments"
                    },
                    {
                        "name": "bowtie2_orientation_PE",
                        "type": "radio",
                        "choices": [
                            {
                                "Not stranded": ""
                            },
                            {
                                "Forward Reverse": "--fr"
                            },
                            {
                                "Reverse Forward": "--rf"
                            },
                            {
                                "Forward Forward": "--ff"
                            }
                        ],
                        "value": "",
                        "label": "The upstream\/downstream mate orientations for a valid paired-end alignment against the forward reference strand."
                    }
                ]
            },
            {
                "name": "bowtie2_SE",
                "cname": "Bowtie2 SE",
                "command": "bowtie2",
                "category": "mapping",
                "output_dir": "bowtie2\/SE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "index",
                        "type": "bowtie2_index",
                        "file": "index",
                        "description": "Index files for bowtie2 alignment"
                    }
                ],
                "outputs": [
                    {
                        "name": "bam",
                        "type": "bams",
                        "file": "{sample}.bam",
                        "description": "Alignment files"
                    }
                ],
                "options": [
                    {
                        "name": "bowtie2_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use to align reads"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "bowtie2": [
                "Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https:\/\/doi.org\/10.1038\/nmeth.1923"
            ],
            "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: bowtie2,\n  name: Bowtie2,\n  article: 10.1038\/nmeth.1923,\n  website: \"http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/index.shtml\",\n  git: \"https:\/\/github.com\/BenLangmead\/bowtie2\",\n  description: \"A fast and sensitive gapped read aligner\",\n  version: \"2.5.1\",\n  documentation: \"http:\/\/bowtie-bio.sourceforge.net\/bowtie2\/manual.shtml\",\n  multiqc: \"bowtie2\",\n  commands:\n    [\n      {\n        name: bowtie2_PE,\n        cname: \"Bowtie2 PE\",\n        command: bowtie2,\n        category: \"mapping\",\n        output_dir: bowtie2\/PE,\n        inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }, { name: index, type: \"bowtie2_index\", file: index, description: \"Index files for bowtie2 alignment\" }],\n        outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n        options:\n          [\n            {\n              name: bowtie2_threads,\n              prefix: --threads,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use to align reads\",\n            },\n            {\n              name: bowtie2_minins_PE,\n              prefix: -I,\n              type: numeric,\n              value: 0,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"The minimum insert size for valid paired-end alignments\",\n            },\n            {\n              name: bowtie2_maxins_PE,\n              prefix: -X,\n              type: numeric,\n              value: 250,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"The maximum insert size for valid paired-end alignments\",\n            },\n            {\n              name: bowtie2_orientation_PE,\n              type: radio,\n              choices:\n                [\n                  Not stranded: \"\",\n                  Forward Reverse: --fr,\n                  Reverse Forward: --rf,\n                  Forward Forward: --ff\n                ],\n              value: \"\",\n              label: \"The upstream\/downstream mate orientations for a valid paired-end alignment against the forward reference strand.\",\n            },\n          ]\n      },\n      {\n        name: bowtie2_SE,\n        cname: \"Bowtie2 SE\",\n        command: bowtie2,\n        category: \"mapping\",\n        output_dir: bowtie2\/SE,\n        inputs: [{ name: read, type: \"reads\" }, { name: index, type: \"bowtie2_index\", file: index, description: \"Index files for bowtie2 alignment\" }],\n        outputs: [{ name: bam, type: \"bams\", file: \"{sample}.bam\", description: \"Alignment files\" }],\n        options:\n          [\n            {\n              name: bowtie2_threads,\n              prefix: --threads,\n              type: numeric,\n              value: 4,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Number of threads to use to align reads\",\n            },\n          ]\n      }\n    ],\n  install:  {\n    # bowtie2: [\n    #   \"wget -O bowtie2-2.4.1-linux-x86_64.zip https:\/\/github.com\/BenLangmead\/bowtie2\/releases\/download\/v2.4.1\/bowtie2-2.4.1-linux-x86_64.zip\",\n    #   \"unzip bowtie2-2.4.1-linux-x86_64.zip\",\n    #   \"cp bowtie2-2.4.1-linux-x86_64\/bowtie2* \/usr\/bin\",\n    #   \"rm -rf bowtie2-2.4.1*\"\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  citations:  {\n    bowtie2: [\n      \"Langmead, B., Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359 (2012). https:\/\/doi.org\/10.1038\/nmeth.1923\"\n    ],\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}"
    }
]