[
    {
        "id": "vcf_annotate",
        "name": "vcf annotate",
        "description": "BCFtools annotate to append a new INFO in a vcf.",
        "version": "1.17",
        "website": "https:\/\/samtools.github.io\/bcftools\/",
        "git": "https:\/\/github.com\/samtools\/bcftools",
        "documentation": "https:\/\/samtools.github.io\/bcftools\/bcftools.html#annotate",
        "article": "10.1093\/bioinformatics\/btr509",
        "multiqc": "custom",
        "commands": [
            {
                "name": "vcf_annotate",
                "cname": "vcf_annotate",
                "command": "bcftools",
                "category": "vcf_postprocess",
                "output_dir": "vcf_annotate",
                "inputs": [
                    {
                        "name": "vcf",
                        "type": "vcf_file",
                        "description": "Variant Calling Format (vcf) file"
                    },
                    {
                        "name": "tsv",
                        "type": "tsv",
                        "description": "TSV file with CHR POS0 INFO_ANNOTATION"
                    }
                ],
                "outputs": [
                    {
                        "name": "vcf_annot",
                        "type": "vcf",
                        "file": "vcf_annotate.vcf",
                        "description": "vcf file whith annotation append"
                    }
                ],
                "options": [
                    {
                        "name": "vcf_annotate_header",
                        "prefix": "-h",
                        "value": "##INFO=<ID=AA,Number=1,Type=String,Description='Ancestral Allele'>",
                        "label": "Info field writen in the vcf header information. Standard format is defined here https:\/\/samtools.github.io\/hts-specs\/VCFv4.2.pdf : ##INFO=<ID={acronym annotation},Number={number of value in INFO field},Type={Type},Description='{Description of the acronym}'>",
                        "type": "text"
                    },
                    {
                        "name": "vcf_annotate_column",
                        "prefix": "-c",
                        "value": "AA",
                        "label": "The third column of the bed file will be writen with this acronym in INFO field of the vcf. i.e AA for Ancestral Allele",
                        "type": "text"
                    },
                    {
                        "name": "vcf_annotate_threads",
                        "prefix": "--threads",
                        "type": "numeric",
                        "value": 4,
                        "min": 1,
                        "max": "NA",
                        "step": 1,
                        "label": "Number of threads to use"
                    }
                ]
            }
        ],
        "install": [],
        "citations": {
            "bcftools": [
                "Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https:\/\/doi.org\/10.1093\/bioinformatics\/btr509"
            ]
        },
        "yaml": "{\n  id: \"vcf_annotate\",\n  name: \"vcf annotate\",\n  description: \"BCFtools annotate to append a new INFO in a vcf.\",\n  version: \"1.17\",\n  website: \"https:\/\/samtools.github.io\/bcftools\/\",\n  git: \"https:\/\/github.com\/samtools\/bcftools\",\n  documentation: \"https:\/\/samtools.github.io\/bcftools\/bcftools.html#annotate\",\n  article: \"10.1093\/bioinformatics\/btr509\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: \"vcf_annotate\",\n        cname: \"vcf_annotate\",\n        command: \"bcftools\",\n        category: vcf_postprocess,\n        output_dir: \"vcf_annotate\",\n        inputs:\n          [\n            { name: \"vcf\", type: \"vcf_file\", description: \"Variant Calling Format (vcf) file\" },\n            { name: \"tsv\", type: \"tsv\", description: \"TSV file with CHR POS0 INFO_ANNOTATION\" },\n          ],\n        outputs:\n          [\n            { name: \"vcf_annot\", type: \"vcf\", file: \"vcf_annotate.vcf\", description: \"vcf file whith annotation append\" },\n          ],\n        options:\n          [\n            {\n              name: \"vcf_annotate_header\",\n              prefix: \"-h\",\n              value: \"##INFO=<ID=AA,Number=1,Type=String,Description='Ancestral Allele'>\",\n              label: \"Info field writen in the vcf header information. Standard format is defined here https:\/\/samtools.github.io\/hts-specs\/VCFv4.2.pdf : ##INFO=<ID={acronym annotation},Number={number of value in INFO field},Type={Type},Description='{Description of the acronym}'>\",\n              type: \"text\",\n            },\n            {\n              name: \"vcf_annotate_column\",\n              prefix: \"-c\",\n              value: \"AA\",\n              label: \"The third column of the bed file will be writen with this acronym in INFO field of the vcf. i.e AA for Ancestral Allele\",\n              type: \"text\",\n            },\n            {\n              name: vcf_annotate_threads,\n              prefix: \"--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      },\n    ],\n  install:\n    {\n      # bcftools:\n      #   [\n      #     \"cd \/opt\/biotools\",\n      #     \"wget https:\/\/github.com\/samtools\/bcftools\/releases\/download\/1.9\/bcftools-1.9.tar.bz2\",\n      #     \"tar -xvjf bcftools-1.9.tar.bz2\",\n      #     \"cd bcftools-1.9\",\n      #     \".\/configure --prefix=\/opt\/biotools\",\n      #     \"make -j 10\",\n      #     \"make install\",\n      #     \"mv bcftools \/opt\/biotools\/bin\/\",\n      #     \"cd .. && rm -r bcftools-1.9.tar.bz2 bcftools-1.9\",\n      #     \"sed -i 's\/python\/python3\/g'  \/opt\/biotools\/bin\/plot-vcfstats\"\n      #   ],\n    },\n  citations:  {\n    bcftools: [\n      \"Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https:\/\/doi.org\/10.1093\/bioinformatics\/btr509\"\n    ],\n  }\n}\n"
    }
]