[
    {
        "id": "gatk3_IndelRealigner",
        "name": "GATK3 Indel Realigner",
        "article": null,
        "website": "https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.6-0\/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php",
        "git": "",
        "description": "The local realignment process is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases is minimized across all the reads.",
        "version": "3.8",
        "documentation": "https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.6-0\/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php",
        "multiqc": "custom",
        "commands": [
            {
                "name": "gatk3_IndelRealigner",
                "cname": "Gatk3 IndelRealigner",
                "command": "gatk3",
                "category": "bam_correction",
                "output_dir": "gatk_IndelRealigner",
                "inputs": [
                    {
                        "name": "bam",
                        "type": "bams"
                    },
                    {
                        "name": "genome_fasta",
                        "type": "contigs"
                    },
                    {
                        "name": "fasta_index",
                        "type": "fasta_index"
                    },
                    {
                        "name": "sequence_dict",
                        "type": "sequence_dict"
                    }
                ],
                "outputs": [
                    {
                        "name": "sorted_bam",
                        "type": "bams",
                        "file": "{sample}.mapped.dedup.realigned.sorted.bam",
                        "description": "Bam with indels realigned"
                    }
                ],
                "options": [
                    {
                        "name": "gatk3_IndelRealigner_threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    },
                    {
                        "name": "gatk3_IndelRealigner_samtools_memory",
                        "type": "numeric",
                        "value": 2,
                        "label": "-m parameter for samtools sort: Memory allocated per thread for samtools_sort (in Gb)."
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "gatk": [
                "McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297\u20111303. https:\/\/doi.org\/10.1101\/gr.107524.110 "
            ]
        },
        "yaml": "{\n  id: gatk3_IndelRealigner,\n  name: GATK3 Indel Realigner,\n  article: ~,\n  website: \"https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.6-0\/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php\",\n  git: \"\",\n  description: \"The local realignment process is designed to consume one or more BAM files and to locally realign reads such that the number of mismatching bases is minimized across all the reads.\",\n  version: \"3.8\",\n  documentation: \"https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.6-0\/org_broadinstitute_gatk_tools_walkers_indels_IndelRealigner.php\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: gatk3_IndelRealigner,\n        cname : \"Gatk3 IndelRealigner\",\n        command: gatk3,\n        category: \"bam_correction\",\n        output_dir: gatk_IndelRealigner,\n        inputs: [\n          { name: bam, type: \"bams\" },\n          { name: genome_fasta, type: \"contigs\" },\n          { name: fasta_index, type: \"fasta_index\" },\n          { name: sequence_dict, type: \"sequence_dict\" }\n        ],\n        outputs:  [\n          { name: sorted_bam, type: \"bams\", file: \"{sample}.mapped.dedup.realigned.sorted.bam\", description: \"Bam with indels realigned\" }\n        ],\n        options:\n          [\n            {\n              name: gatk3_IndelRealigner_threads,\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: gatk_IndelRealigner_genome_fasta,\n            #  type: input_file,\n            #  value: \"\",\n            #  label: \"Path to reference genome fasta file\",\n            #},\n            {\n              name: \"gatk3_IndelRealigner_samtools_memory\",\n              type: numeric,\n              value: 2,\n              label: \"-m parameter for samtools sort: Memory allocated per thread for samtools_sort (in Gb).\",\n            },\n          ],\n      },\n    ],\n  install: {\n    # gatk3: [\n    #   \"cd \/opt\/biotools\",\n    #   \"wget -O GenomeAnalysisTK-3.6-0.tar.bz2 'https:\/\/storage.googleapis.com\/gatk-software\/package-archive\/gatk\/GenomeAnalysisTK-3.6-0-g89b7209.tar.bz2'\",\n    #   \"mkdir gatk3\",\n    #   \"tar -C gatk3 -xjf GenomeAnalysisTK-3.6-0.tar.bz2\",\n    #   \"rm GenomeAnalysisTK-3.6-0.tar.bz2\",\n    #   \"rm -r gatk3\/resources\"\n    # ],\n    # java8: [\n    #   \"apt -y update && apt install -y openjdk-8-jre\"\n    # ]\n  },\n  citations:  {\n    gatk: [\n      \"McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297\u20111303. https:\/\/doi.org\/10.1101\/gr.107524.110 \"\n    ],\n  }\n}\n"
    }
]