[
    {
        "id": "flash",
        "name": "FLASH",
        "description": "FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments",
        "version": "1.2.11",
        "website": "https:\/\/ccb.jhu.edu\/software\/FLASH\/",
        "git": "https:\/\/sourceforge.net\/projects\/flashpage\/files\/",
        "documentation": "https:\/\/ccb.jhu.edu\/software\/FLASH\/",
        "article": "10.1093\/bioinformatics\/btr507",
        "multiqc": "flash",
        "commands": [
            {
                "name": "flash",
                "cname": "Flash",
                "command": "flash",
                "category": "sequence_manipulation",
                "output_dir": "flash",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "extendedFrags",
                        "type": [
                            "fastq",
                            "fq.gz"
                        ],
                        "file": "{sample}.extendedFrags.fastq",
                        "description": "The merged reads."
                    },
                    {
                        "name": "notCombined_1",
                        "type": [
                            "fastq",
                            "fq.gz"
                        ],
                        "file": "{sample}.notCombined_1.fastq",
                        "description": "Read 1 of mate pairs that were not merged."
                    },
                    {
                        "name": "notCombined_2",
                        "type": [
                            "fastq",
                            "fq.gz"
                        ],
                        "file": "{sample}.notCombined_2.fastq",
                        "description": "Read 2 of mate pairs that were not merged."
                    },
                    {
                        "name": "hist",
                        "type": "hist",
                        "file": "{sample}.hist",
                        "description": "Numeric histogram of merged read lengths."
                    },
                    {
                        "name": "histogram",
                        "type": "histogram",
                        "file": "{sample}.histogram",
                        "description": "Visual histogram of merged read lengths."
                    }
                ],
                "options": [
                    {
                        "name": "flash_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "flash_min_overlap",
                        "prefix": "-m",
                        "type": "numeric",
                        "value": 10,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "-m : The minimum required overlap length between two reads to provide a confident overlap"
                    },
                    {
                        "name": "flash_max_overlap",
                        "prefix": "-M",
                        "type": "numeric",
                        "value": 65,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "-M : Maximum overlap length expected in approximately 90% of read pairs"
                    },
                    {
                        "name": "flash_max_mismatch_density",
                        "prefix": "-x",
                        "type": "numeric",
                        "value": 0.25,
                        "min": "NA",
                        "max": "NA",
                        "step": "NA",
                        "label": "-x : Maximum allowed ratio between the number of mismatched base pairs and the overlap length"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "FLASH": [
                "Tanja Mago\u010d, Steven L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2957-2963, https:\/\/doi.org\/10.1093\/bioinformatics\/btr507"
            ]
        },
        "yaml": "{\n  id: flash,\n  name: FLASH,\n  description: \"FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments\",\n  version: \"1.2.11\",\n  website: \"https:\/\/ccb.jhu.edu\/software\/FLASH\/\",\n  git: \"https:\/\/sourceforge.net\/projects\/flashpage\/files\/\",\n  documentation: \"https:\/\/ccb.jhu.edu\/software\/FLASH\/\",\n  article: 10.1093\/bioinformatics\/btr507,\n  multiqc: \"flash\",\n  commands:\n    [\n      {\n        name: flash,\n        cname: \"Flash\",\n        command: flash,\n        category: \"sequence_manipulation\",\n        output_dir: flash,\n        inputs: [{ name: read, type: \"reads\" },{ name: read2, type: \"reads\" }],\n        outputs: [\n          { name: extendedFrags, type: [\"fastq\", \"fq.gz\"], file: \"{sample}.extendedFrags.fastq\", description: \"The merged reads.\" },\n          { name: notCombined_1, type: [\"fastq\", \"fq.gz\"], file: \"{sample}.notCombined_1.fastq\", description: \"Read 1 of mate pairs that were not merged.\" },\n          { name: notCombined_2, type: [\"fastq\", \"fq.gz\"], file: \"{sample}.notCombined_2.fastq\", description: \"Read 2 of mate pairs that were not merged.\" },\n          { name: hist, type: \"hist\", file: \"{sample}.hist\", description: \"Numeric histogram of merged read lengths.\" },\n          { name: histogram, type: \"histogram\", file: \"{sample}.histogram\", description: \"Visual histogram of merged read lengths.\" }\n        ],\n        options:\n          [\n            {\n              name: flash_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: flash_min_overlap,\n              prefix: -m,\n              type: numeric,\n              value: 10,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"-m : The minimum required overlap length between two reads to provide a confident overlap\",\n            },\n            {\n              name: flash_max_overlap,\n              prefix: -M,\n              type: numeric,\n              value: 65,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"-M : Maximum overlap length expected in approximately 90% of read pairs\",\n            },\n            {\n              name: flash_max_mismatch_density,\n              prefix: -x,\n              type: numeric,\n              value: 0.25,\n              min: NA,\n              max: NA,\n              step: NA,\n              label: \"-x : Maximum allowed ratio between the number of mismatched base pairs and the overlap length\",\n            },\n          ],\n      },\n    ],\n  #prepare_report_script:  flash.prepare.report.py, # No more needed with MultiQC 1.9\n  #prepare_report_outputs: [\n  #  flash_combinations_mqc.csv\n  #],\n  install: {\n    # FLASH: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget -O FLASH-1.2.11.tar.gz https:\/\/sourceforge.net\/projects\/flashpage\/files\/FLASH-1.2.11.tar.gz\",\n    #   \"tar -xvzf FLASH-1.2.11.tar.gz\",\n    #   \"cd FLASH-1.2.11\",\n    #   \"make\",\n    #   \"mv flash ..\/bin\",\n    #   \"cd ..\",\n    #   \"rm -r FLASH-1.2.11 FLASH-1.2.11.tar.gz\"\n    # ]\n  },\n  citations:  {\n    FLASH: [\n      \"Tanja Mago\u010d, Steven L. Salzberg, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2957-2963, https:\/\/doi.org\/10.1093\/bioinformatics\/btr507\"\n    ],\n  }\n}\n"
    }
]