[
    {
        "id": "radsex_process",
        "name": "radsex_process",
        "article": "https:\/\/doi.org\/10.1111\/1755-0998.13360",
        "website": "https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1111\/1755-0998.13360",
        "git": "https:\/\/github.com\/SexGenomicsToolkit\/radsex",
        "description": "Creating a table of marker depths from processed radtag reads",
        "version": "latest",
        "documentation": "https:\/\/sexgenomicstoolkit.github.io\/html\/radsex\/introduction.html",
        "multiqc": "custom",
        "commands": [
            {
                "name": "radsex_process",
                "command": "\/opt\/biotools\/radsex\/bin\/radsex process",
                "category": "radsex",
                "output_dir": "radsex_process",
                "inputs": [
                    {
                        "name": "read_dir",
                        "type": "SE_read_dir",
                        "description": "Directory containing the processed radtag reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "markers_table",
                        "type": "tsv",
                        "file": "markers_table.tsv",
                        "description": "Table containing the depth of each marker in each individual (tabulated file)"
                    }
                ],
                "options": [
                    {
                        "name": "radsex_threads",
                        "prefix": "--threads",
                        "value": 16,
                        "min": 1,
                        "max": 64,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    },
                    {
                        "name": "radsex_min_depth",
                        "prefix": "--min-depth",
                        "value": 1,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum depth to consider a marker present in an individual",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "install": {
            "radsex_apt_dependencies": [
                "apt-get update",
                "apt-get install -y gcc zlib1g-dev pkg-config libfreetype6-dev libpng-dev"
            ],
            "radsex": [
                "cd \/opt\/biotools",
                "git clone https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/radsex",
                "cd radsex",
                "make -j 10"
            ],
            "sgtr": [
                "Rscript -e 'devtools::install_github(\"SexGenomicsToolkit\/sgtr\");library(\"sgtr\")'"
            ]
        },
        "citations": {
            "radsex": [
                "Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., et al. (2021), RADSex: A computational workflow to study sex determination using restriction site\u2010associated DNA sequencing data. Mol Ecol Resour. https:\/\/doi.org\/10.1111\/1755-0998.13360"
            ]
        },
        "yaml": "{\n  id: radsex_process,\n  name: radsex_process,\n  article:  \"https:\/\/doi.org\/10.1111\/1755-0998.13360\",\n  website: \"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1111\/1755-0998.13360\",\n  git: \"https:\/\/github.com\/SexGenomicsToolkit\/radsex\",\n  description: \"Creating a table of marker depths from processed radtag reads\",\n  version: \"latest\",\n  documentation: \"https:\/\/sexgenomicstoolkit.github.io\/html\/radsex\/introduction.html\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: radsex_process,\n        command: \/opt\/biotools\/radsex\/bin\/radsex process,\n        category: \"radsex\",\n        output_dir: radsex_process,\n        inputs: [\n          #{ name: reads_demultiplexed, type: \"fq.gz\", file: \"{individu}.fastq.gz\", description: \"Files of reads for each individual\" },\n          { name: \"read_dir\", type: \"SE_read_dir\", description: \"Directory containing the processed radtag reads\" },\n        ],\n        outputs:\n          [\n            { name: markers_table, type: \"tsv\", file: \"markers_table.tsv\", description: \"Table containing the depth of each marker in each individual (tabulated file)\" }\n          ],\n        options:\n          [\n            {\n              name: \"radsex_threads\",\n              prefix: \"--threads\",\n              value: 16,\n              min: 1,\n              max: 64,\n              step: 1,\n              label: \"Threads to use\",\n              type: \"numeric\",\n            },\n            {\n              name: \"radsex_min_depth\",\n              prefix: \"--min-depth\",\n              value: 1,\n              min: 1,\n              max: NA,\n              step: 1,\n              label: \"Minimum depth to consider a marker present in an individual\",\n              type: \"numeric\",\n            },\n          ],\n      },\n    ],\n  # prepare_report_script:  radsex_process.prepare.report.R,\n  # prepare_report_outputs: [\n  #   Marker_depth_radsex_process_mqc.png,\n  # ],\n  install:\n    {\n      radsex_apt_dependencies: [\n        \"apt-get update\",\n        \"apt-get install -y gcc zlib1g-dev pkg-config libfreetype6-dev libpng-dev\"\n      ],\n      radsex: [\n        \"cd \/opt\/biotools\",\n        \"git clone https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/radsex\",\n        \"cd radsex\",\n        \"make -j 10\",\n      ],\n      sgtr: [\n        'Rscript -e ''devtools::install_github(\"SexGenomicsToolkit\/sgtr\");library(\"sgtr\")'''\n      ],\n    },\n    citations:  {\n      radsex: [\n        \"Feron, R., Pan, Q., Wen, M., Imarazene, B., Jouanno, E., Anderson, J., Herpin, A., et al. (2021), RADSex: A computational workflow to study sex determination using restriction site\u2010associated DNA sequencing data. Mol Ecol Resour. https:\/\/doi.org\/10.1111\/1755-0998.13360\"\n      ]\n    }\n}\n"
    }
]