[
    {
        "id": "gatk3_prepare_fasta",
        "name": "GATK3 prepare fasta",
        "article": null,
        "website": "",
        "git": "",
        "description": "Prepare fasta ref for GATK",
        "version": "3.0",
        "documentation": "",
        "multiqc": "custom",
        "commands": [
            {
                "name": "gatk3_prepare_fasta",
                "cname": "gatk3 prepare fasta",
                "command": "",
                "category": "indexing",
                "output_dir": "gatk_prepare_fasta",
                "inputs": [
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "fasta",
                        "type": "contigs",
                        "file": "ref.fasta",
                        "description": "Reference fasta"
                    },
                    {
                        "name": "index",
                        "type": "fasta_index",
                        "file": "ref.fai",
                        "description": "Reference index"
                    },
                    {
                        "name": "fadict",
                        "type": "sequence_dict",
                        "file": "ref.dict",
                        "description": "Reference dict"
                    }
                ],
                "options": [
                    {
                        "name": "gatk3_prepare_fasta_genome_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to reference genome fasta file"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "picard_tools": [
                "Picard Toolkit. 2019. Broad Institute, GitHub Repository. http:\/\/broadinstitute.github.io\/picard\/; Broad Institute"
            ],
            "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\u20132079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352"
            ]
        },
        "yaml": "{\n  id: gatk3_prepare_fasta,\n  name: GATK3 prepare fasta,\n  article: ~,\n  website: \"\",\n  git: \"\",\n  description: \"Prepare fasta ref for GATK\",\n  version: \"3.0\",\n  documentation: \"\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: gatk3_prepare_fasta,\n        cname : \"gatk3 prepare fasta\",\n        command: \"\",\n        category: \"indexing\",\n        output_dir: gatk_prepare_fasta,\n        inputs: [{ name: genome_fasta, type: \"contigs\", from: \"parameter\"}],\n        outputs:  [\n          { name: fasta, type: \"contigs\", file: \"ref.fasta\", description: \"Reference fasta\" },\n          { name: index, type: \"fasta_index\", file: \"ref.fai\", description: \"Reference index\" },\n          { name: fadict, type: \"sequence_dict\", file: \"ref.dict\", description: \"Reference dict\" },\n        ],\n        options:\n          [\n            {\n              name: gatk3_prepare_fasta_genome_fasta,\n              type: input_file,\n              value: \"\",\n              label: \"Path to reference genome fasta file\",\n            },\n          ],\n      },\n    ],\n  install: {\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    # picard_tools: [\n    #   \"cd \/opt\/biotools\/bin\",\n    #   \"wget https:\/\/github.com\/broadinstitute\/picard\/releases\/download\/2.20.8\/picard.jar\"\n    # ],\n  },\n  citations:  {\n    picard_tools: [\n      \"Picard Toolkit. 2019. Broad Institute, GitHub Repository. http:\/\/broadinstitute.github.io\/picard\/; Broad Institute\"\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\u20132079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n    ]\n  }\n}\n"
    }
]