[
    {
        "id": "ustacks",
        "name": "ustacks",
        "article": "10.1111\/mec.15253",
        "website": "http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/ustacks.php",
        "git": "",
        "description": "The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks (or putative alleles). Comparing the stacks it will form a set of putative loci and detect SNPs at each locus using a maximum likelihood framework.",
        "version": "2.64",
        "documentation": "http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/ustacks.php",
        "multiqc": "custom",
        "commands": [
            {
                "name": "ustacks",
                "cname": "Ustacks",
                "command": "ustacks",
                "category": "stacks",
                "output_dir": "stacks",
                "inputs": [
                    {
                        "name": "read_dir",
                        "type": "SE_read_dir",
                        "description": "A dir containing fastq.gz or fq.gz files"
                    }
                ],
                "outputs": [
                    {
                        "name": "ustacks_done",
                        "type": "ustacks_done",
                        "file": "",
                        "description": "in dir containing ustacks results"
                    }
                ],
                "options": [
                    {
                        "name": "ustacks_threads",
                        "prefix": "-p",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "ustacks_M",
                        "prefix": "-M",
                        "type": "numeric",
                        "value": 2,
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "Maximum distance (in nucleotides) allowed between stacks"
                    },
                    {
                        "name": "ustacks_m",
                        "prefix": "-m",
                        "type": "numeric",
                        "value": 3,
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "Minimum depth of coverage required to create a stack"
                    },
                    {
                        "name": "ustacks_N",
                        "prefix": "-N",
                        "type": "numeric",
                        "value": "NA",
                        "min": 0,
                        "max": "NA",
                        "step": 1,
                        "label": "Maximum distance allowed to align secondary reads to primary stacks (default: M + 2)"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "stacks": [
                "Rochette, NC, Rivera-Col\u00f3n, AG, Catchen, JM. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol Ecol. 2019; 28: 4737- 4754. https:\/\/doi.org\/10.1111\/mec.15253"
            ]
        },
        "yaml": "{\n  id: ustacks,\n  name: ustacks,\n  article: 10.1111\/mec.15253,\n  website: \"http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/ustacks.php\",\n  git: \"\",\n  description: \"The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks (or putative alleles). Comparing the stacks it will form a set of putative loci and detect SNPs at each locus using a maximum likelihood framework.\",\n  version: \"2.64\",\n  documentation: \"http:\/\/catchenlab.life.illinois.edu\/stacks\/comp\/ustacks.php\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: ustacks,\n        cname: \"Ustacks\",\n        command: ustacks,\n        category: \"stacks\",\n        output_dir: stacks,\n        inputs: [\n          { name: read_dir, type: \"SE_read_dir\", description: \"A dir containing fastq.gz or fq.gz files\"}\n          ],\n        outputs:\n          [\n            { name: \"ustacks_done\", type: \"ustacks_done\", file: \"\", description: \"in dir containing ustacks results\" },\n          ],\n        options:\n          [\n            {\n              name: ustacks_threads,\n              prefix: -p,\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: ustacks_M,\n              prefix: -M,\n              type: numeric,\n              value: 2,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"Maximum distance (in nucleotides) allowed between stacks\",\n            },\n            {\n              name: ustacks_m,\n              prefix: -m,\n              type: numeric,\n              value: 3,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"Minimum depth of coverage required to create a stack\",\n            },\n            {\n              name: ustacks_N,\n              prefix: -N,\n              type: numeric,\n              value: NA,\n              min: 0,\n              max: NA,\n              step: 1,\n              label: \"Maximum distance allowed to align secondary reads to primary stacks (default: M + 2)\",\n            },\n          ],\n      },\n    ],\n  install:\n    {\n      # stacks: [\n      #   \"cd \/opt\/biotools\",\n      #   \"wget http:\/\/catchenlab.life.illinois.edu\/stacks\/source\/stacks-2.61.tar.gz\",\n      #   \"tar -zxvf stacks-2.61.tar.gz\",\n      #   \"cd stacks-2.61\/\",\n      #   \".\/configure\",\n      #   \"make -j 10\",\n      #   \"make install\",\n      #   \"mv -t ..\/bin sstacks kmer_filter gstacks tsv2bam process_shortreads populations ustacks phasedstacks cstacks process_radtags\",\n      #   \"cd .. && rm -r stacks-2.61 stacks-2.61.tar.gz\"\n      # ]\n    },\n  citations:  {\n    stacks: [\n      \"Rochette, NC, Rivera-Col\u00f3n, AG, Catchen, JM. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol Ecol. 2019; 28: 4737- 4754. https:\/\/doi.org\/10.1111\/mec.15253\"\n    ]\n  }\n}\n"
    }
]