[
    {
        "id": "dada2_Err_Derep_makeSequenceTable",
        "name": "dada2_Err_Derep_makeSequenceTable",
        "article": "10.1038\/nmeth.3869",
        "website": "https:\/\/benjjneb.github.io\/dada2",
        "git": "https:\/\/github.com\/benjjneb\/dada2",
        "description": "Learn the Error Rates, dereplicate, Merge paired reads, Construct sequence table and Remove chimeras",
        "version": "1.26",
        "documentation": "https:\/\/benjjneb.github.io\/dada2",
        "multiqc": "custom",
        "commands": [
            {
                "name": "dada2_Err_Derep_makeSequenceTable_PE",
                "cname": "dada2_Err_Derep_makeSequenceTable PE",
                "command": null,
                "category": "metabarcoding",
                "output_dir": "dada2_Err_Derep_makeSequenceTable\/PE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "ASVseqfile",
                        "type": "fasta_file",
                        "file": "ASVseqs.fasta",
                        "description": "amplicon sequence variants in fasta "
                    },
                    {
                        "name": "ASVtable",
                        "type": "tsv",
                        "file": "ASVabundance.tsv",
                        "description": "number of times each exact amplicon sequence was observed in each sample"
                    },
                    {
                        "name": "errRplotF",
                        "type": "png",
                        "file": "errorProfilePlotF_mqc.png",
                        "description": "error profile plot forward"
                    },
                    {
                        "name": "errRplotR",
                        "type": "png",
                        "file": "qerrorProfilePlotR_mqc.png",
                        "description": "error profile plot reverse"
                    }
                ],
                "options": [
                    {
                        "name": "dada2_Err_Derep_makeSequenceTable_remove_chim",
                        "prefix": null,
                        "type": "checkbox",
                        "value": true,
                        "label": "Remove chimeras"
                    }
                ]
            },
            {
                "name": "dada2_Err_Derep_makeSequenceTable_SE",
                "cname": "dada2_Err_Derep_makeSequenceTable SE",
                "command": null,
                "category": "metabarcoding",
                "output_dir": "dada2_Err_Derep_makeSequenceTable\/SE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "ASVseqfile",
                        "type": "fasta_file",
                        "file": "ASVseqs.fasta",
                        "description": "amplicon sequence variants in fasta "
                    },
                    {
                        "name": "ASVtable",
                        "type": "tsv",
                        "file": "ASVabundance.tsv",
                        "description": "number of times each exact amplicon sequence was observed in each sample"
                    },
                    {
                        "name": "errRplotF",
                        "type": "png",
                        "file": "errorProfilePlot_mqc.png",
                        "description": "error profile plot forward"
                    }
                ],
                "options": [
                    {
                        "name": "dada2_Err_Derep_makeSequenceTable_remove_chim",
                        "prefix": null,
                        "type": "checkbox",
                        "value": true,
                        "label": "Remove chimeras"
                    }
                ]
            }
        ],
        "script": "dada2_Err_Derep_makeSequenceTable.script.R",
        "install": [],
        "citations": {
            "dada2": [
                "Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038\/nmeth.3869"
            ]
        },
        "yaml": "{\n  id: dada2_Err_Derep_makeSequenceTable,\n  name: dada2_Err_Derep_makeSequenceTable,\n  article: 10.1038\/nmeth.3869,\n  website: \"https:\/\/benjjneb.github.io\/dada2\",\n  git: \"https:\/\/github.com\/benjjneb\/dada2\",\n  description: \"Learn the Error Rates, dereplicate, Merge paired reads, Construct sequence table and Remove chimeras\",\n  version: \"1.26\",\n  documentation: \"https:\/\/benjjneb.github.io\/dada2\",\n  multiqc:  \"custom\",\n  commands:\n    [\n      {\n        name: dada2_Err_Derep_makeSequenceTable_PE,\n        cname: \"dada2_Err_Derep_makeSequenceTable PE\",\n        command: ~,\n        category: \"metabarcoding\",\n        output_dir: dada2_Err_Derep_makeSequenceTable\/PE,\n        inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }],\n        outputs:  [          \n           { name: ASVseqfile, type: \"fasta_file\", file: \"ASVseqs.fasta\", description: \"amplicon sequence variants in fasta \" },\n           { name: ASVtable, type: \"tsv\", file: \"ASVabundance.tsv\", description: \"number of times each exact amplicon sequence was observed in each sample\" },\n           { name: errRplotF, type: \"png\", file: \"errorProfilePlotF_mqc.png\", description: \"error profile plot forward\" },\n           { name: errRplotR, type: \"png\", file: \"qerrorProfilePlotR_mqc.png\", description: \"error profile plot reverse\" },\n        ],\n        options:\n          [\n           {\n              name: dada2_Err_Derep_makeSequenceTable_remove_chim,\n              prefix: ,\n              type: checkbox,\n              value: TRUE,\n              label: \"Remove chimeras\",\n            },\n          ],\n      },\n      {\n        name: dada2_Err_Derep_makeSequenceTable_SE,\n        cname: \"dada2_Err_Derep_makeSequenceTable SE\",\n        command: ~,\n        category: \"metabarcoding\",\n        output_dir: dada2_Err_Derep_makeSequenceTable\/SE,\n        inputs: [{ name: read, type: \"reads\" },],\n        outputs:  [          \n           { name: ASVseqfile, type: \"fasta_file\", file: \"ASVseqs.fasta\", description: \"amplicon sequence variants in fasta \" },\n           { name: ASVtable, type: \"tsv\", file: \"ASVabundance.tsv\", description: \"number of times each exact amplicon sequence was observed in each sample\" },\n           { name: errRplotF, type: \"png\", file: \"errorProfilePlot_mqc.png\", description: \"error profile plot forward\" },\n        ],\n        options:\n          [\n            {\n              name: dada2_Err_Derep_makeSequenceTable_remove_chim,\n              prefix: ,\n              type: checkbox,\n              value: TRUE,\n              label: \"Remove chimeras\",\n            },\n          ],\n      },\n    ],\n  script: dada2_Err_Derep_makeSequenceTable.script.R,  \n  install: {\n    # dada2: [\n    #   \"Rscript -e 'library(\\\"devtools\\\");devtools::install_github(\\\"benjjneb\/dada2\\\", ref=\\\"v1.18\\\");library(\\\"dada2\\\")'\",\n    # ],\n  },\n  citations:  {\n    dada2: [\n      \"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581-583. doi:10.1038\/nmeth.3869\"\n    ],\n  }\n}\n"
    }
]