[
    {
        "id": "minimap2_overlap",
        "name": "minimap2 overlap",
        "article": "10.1093\/bioinformatics\/bty191",
        "website": "https:\/\/lh3.github.io\/minimap2\/",
        "git": "https:\/\/github.com\/lh3\/minimap2",
        "description": "A versatile pairwise aligner for genomic and spliced nucleotide sequences",
        "version": "2.26",
        "documentation": "https:\/\/github.com\/lh3\/minimap2\/blob\/master\/README.md",
        "multiqc": "custom",
        "commands": [
            {
                "name": "minimap2_overlap",
                "cname": "Minimap2 overlap",
                "command": "minimap2 -x",
                "category": "mapping",
                "output_dir": "minimap2_overlap",
                "inputs": [
                    {
                        "name": "minimap2_overlap_file_1",
                        "type": [
                            "reads",
                            "fasta"
                        ],
                        "description": "Path to the first reads file to find overlaps"
                    },
                    {
                        "name": "minimap2_overlap_file_2",
                        "type": [
                            "reads",
                            "fasta"
                        ],
                        "description": "Path to the second reads file to find overlaps (can be the same file as file 1)"
                    }
                ],
                "outputs": [
                    {
                        "name": "reads_overlaps",
                        "type": "paf.gz",
                        "file": "reads.paf.gz",
                        "description": "Reads overlaps"
                    }
                ],
                "options": [
                    {
                        "name": "minimap2_overlap_threads",
                        "prefix": "-t",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "minimap2_overlap_file_1",
                        "type": "input_file",
                        "value": "",
                        "multiple": false,
                        "label": "Path to the first reads file to find overlaps"
                    },
                    {
                        "name": "minimap2_overlap_file_2",
                        "type": "input_file",
                        "value": "",
                        "multiple": false,
                        "label": "Path to the second reads file to find overlaps (can be the same file as file 1)"
                    },
                    {
                        "name": "minimap2_overlap_pacbio_oxfordNanopore",
                        "type": "radio",
                        "value": "ont",
                        "choices": [
                            {
                                "Pacbio": "pb"
                            },
                            {
                                "Oxford Nanopore": "ont"
                            }
                        ],
                        "label": "Sequencing used to produce reads"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "minimap2": [
                "Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, 15 September 2018, Pages 3094-3100, https:\/\/doi.org\/10.1093\/bioinformatics\/bty191"
            ]
        },
        "yaml": "{\n  id: minimap2_overlap,\n  name: minimap2 overlap,\n  article: \"10.1093\/bioinformatics\/bty191\",\n  website: \"https:\/\/lh3.github.io\/minimap2\/\",\n  git: \"https:\/\/github.com\/lh3\/minimap2\",\n  description: \"A versatile pairwise aligner for genomic and spliced nucleotide sequences\",\n  version: \"2.26\",\n  documentation: \"https:\/\/github.com\/lh3\/minimap2\/blob\/master\/README.md\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: minimap2_overlap,\n        cname: \"Minimap2 overlap\",\n        command:  minimap2 -x ,\n        category: \"mapping\",\n        output_dir: minimap2_overlap,\n        inputs: [ { name: minimap2_overlap_file_1, type: [\"reads\", \"fasta\"], description: \"Path to the first reads file to find overlaps\" }, { name: minimap2_overlap_file_2, type: [\"reads\", \"fasta\"], description: \"Path to the second reads file to find overlaps (can be the same file as file 1)\" } ],\n        outputs:\n        [\n          { name: reads_overlaps, type: \"paf.gz\", file: reads.paf.gz , description: \"Reads overlaps\" }\n        ],\n        options:\n          [\n            {\n              name: minimap2_overlap_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: minimap2_overlap_file_1,\n              type: input_file,\n              value: \"\",\n              multiple: FALSE,\n              label: \"Path to the first reads file to find overlaps\",\n            },\n            {\n              name: minimap2_overlap_file_2,\n              type: input_file,\n              value: \"\",\n              multiple: FALSE,\n              label: \"Path to the second reads file to find overlaps (can be the same file as file 1)\",\n            },\n            {\n              name: \"minimap2_overlap_pacbio_oxfordNanopore\",\n              type: \"radio\",\n              value: \"ont\",\n              choices: [Pacbio: pb, Oxford Nanopore: ont],\n              label: \"Sequencing used to produce reads\",\n            }\n          ],\n      },\n    ],\n  install: {\n    # minimap2: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget https:\/\/github.com\/lh3\/minimap2\/releases\/download\/v2.17\/minimap2-2.17_x64-linux.tar.bz2\",\n    #   \"tar -xvjf minimap2-2.17_x64-linux.tar.bz2\",\n    #   \"rm minimap2-2.17_x64-linux.tar.bz2\",\n    #   \"ENV PATH \/opt\/biotools\/minimap2-2.17_x64-linux:$PATH\"\n    # ]\n  },\n  citations:  {\n    minimap2: [\n      \"Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, 15 September 2018, Pages 3094-3100, https:\/\/doi.org\/10.1093\/bioinformatics\/bty191\"\n    ]\n  }\n}\n"
    }
]