[
    {
        "id": "dada2_filter_trim",
        "name": "dada2_filter_trim",
        "article": "10.1038\/nmeth.3869",
        "website": "https:\/\/benjjneb.github.io\/dada2",
        "git": "https:\/\/github.com\/benjjneb\/dada2",
        "description": "Fast and accurate sample inference from amplicon data with single-nucleotide resolution",
        "version": "1.26",
        "documentation": "https:\/\/benjjneb.github.io\/dada2",
        "multiqc": "krona_iframe",
        "commands": [
            {
                "name": "dada2_filter_trim_PE",
                "cname": "dada2_filter_trim PE",
                "command": null,
                "category": "metabarcoding",
                "output_dir": "dada2_filter_trim\/PE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    },
                    {
                        "name": "read2",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "filtFs",
                        "type": "fq.gz",
                        "file": "filtered\/{sample}_filt_R1.fastq.gz",
                        "description": "List of filtered forward reads"
                    },
                    {
                        "name": "filtRs",
                        "type": "fq.gz",
                        "file": "filtered\/{sample}_filt_R2.fastq.gz",
                        "description": "List of filtered reverse reads"
                    }
                ],
                "options": [
                    {
                        "name": "dada2_filter_trim_truncLen_forward",
                        "type": "numeric",
                        "value": 220,
                        "min": 0,
                        "max": 400,
                        "step": 1,
                        "label": "truncLen forward : Truncate reads after truncLen bases. Reads shorter than this are discarded"
                    },
                    {
                        "name": "dada2_filter_trim_truncLen_reverse",
                        "type": "numeric",
                        "value": 220,
                        "min": 0,
                        "max": 400,
                        "step": 1,
                        "label": "truncLen reverse : Truncate reads after truncLen bases. Reads shorter than this are discarded"
                    },
                    {
                        "name": "dada2_filter_trim_maxEE_forward",
                        "type": "numeric",
                        "value": 2,
                        "min": -1,
                        "max": "NA",
                        "step": 1,
                        "label": "maxEE forward : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering)."
                    },
                    {
                        "name": "dada2_filter_trim_maxEE_reverse",
                        "type": "numeric",
                        "value": 2,
                        "min": -1,
                        "max": "NA",
                        "step": 1,
                        "label": "maxEE reverse : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering)."
                    }
                ]
            },
            {
                "name": "dada2_filter_trim_SE",
                "cname": "dada2_filter_trim SE",
                "command": null,
                "category": "metabarcoding",
                "output_dir": "dada2_filter_trim\/SE",
                "inputs": [
                    {
                        "name": "read",
                        "type": "reads"
                    }
                ],
                "outputs": [
                    {
                        "name": "filtFs",
                        "type": "fq.gz",
                        "file": "filtered\/{sample}_filt_R1.fastq.gz",
                        "description": "List of filtered forward reads"
                    }
                ],
                "options": [
                    {
                        "name": "dada2_filter_trim_SE_truncLen",
                        "type": "numeric",
                        "value": 220,
                        "min": 1,
                        "max": 400,
                        "step": 1,
                        "label": "truncLen single end read : Truncate reads after truncLen bases. Reads shorter than this are discarded"
                    },
                    {
                        "name": "dada2_filter_trim_SE_maxEE",
                        "type": "numeric",
                        "value": 2,
                        "min": -1,
                        "max": "NA",
                        "step": 1,
                        "label": "maxEE single end read : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering)."
                    }
                ]
            }
        ],
        "script": "dada2_filter_trim.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_filter_trim,\n  name: dada2_filter_trim,\n  article: 10.1038\/nmeth.3869,\n  website: \"https:\/\/benjjneb.github.io\/dada2\",\n  git: \"https:\/\/github.com\/benjjneb\/dada2\",\n  description: \"Fast and accurate sample inference from amplicon data with single-nucleotide resolution\",\n  version: \"1.26\",\n  documentation: \"https:\/\/benjjneb.github.io\/dada2\",\n  multiqc:  \"krona_iframe\",\n  commands:\n    [\n      {\n        name: dada2_filter_trim_PE,\n        cname: \"dada2_filter_trim PE\",\n        command: ~,\n        category: \"metabarcoding\",\n        output_dir: dada2_filter_trim\/PE,\n        inputs: [{ name: read, type: \"reads\" }, { name: read2, type: \"reads\" }],\n        outputs:  [          \n          { name: filtFs, type: \"fq.gz\", file: \"filtered\/{sample}_filt_R1.fastq.gz\", description: \"List of filtered forward reads\" },\n          { name: filtRs, type: \"fq.gz\", file: \"filtered\/{sample}_filt_R2.fastq.gz\", description: \"List of filtered reverse reads\" },\n        ],\n        options:\n          [\n          {\n              name: dada2_filter_trim_truncLen_forward,\n              type: numeric,\n              value: 220,\n              min: 0,\n              max: 400,\n              step: 1,\n              label: \"truncLen forward : Truncate reads after truncLen bases. Reads shorter than this are discarded\",\n            },\n            {\n              name: dada2_filter_trim_truncLen_reverse,\n              type: numeric,\n              value: 220,\n              min: 0,\n              max: 400,\n              step: 1,\n              label: \"truncLen reverse : Truncate reads after truncLen bases. Reads shorter than this are discarded\",\n            },\n            {\n              name: dada2_filter_trim_maxEE_forward,\n              type: numeric,\n              value: 2,\n              min: -1,\n              max: NA,\n              step: 1,\n              label: \"maxEE forward : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering).\",\n            },\n            {\n              name: dada2_filter_trim_maxEE_reverse,\n              type: numeric,\n              value: 2,\n              min: -1,\n              max: NA,\n              step: 1,\n              label: \"maxEE reverse : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering).\",\n            },\n          ],\n      },\n      {\n        name: dada2_filter_trim_SE,\n        cname: \"dada2_filter_trim SE\",\n        command: ~,\n        category: \"metabarcoding\",\n        output_dir: dada2_filter_trim\/SE,\n        inputs: [{ name: read, type: \"reads\" },],\n        outputs:  [          \n          { name: filtFs, type: \"fq.gz\", file: \"filtered\/{sample}_filt_R1.fastq.gz\", description: \"List of filtered forward reads\" },\n        ],\n        options:\n          [\n           {\n              name: dada2_filter_trim_SE_truncLen,\n              type: numeric,\n              value: 220,\n              min: 1,\n              max: 400,\n              step: 1,\n              label: \"truncLen single end read : Truncate reads after truncLen bases. Reads shorter than this are discarded\",\n            },\n            {\n              name: dada2_filter_trim_SE_maxEE,\n              type: numeric,\n              value: 2,\n              min: -1,\n              max: NA,\n              step: 1,\n              label: \"maxEE single end read : After truncation, reads with higher than maxEE 'expected errors' will be discarded. Expected errors are calculated from the nominal definition of the quality score: EE = sum(10^(-Q\/10)). Type -1 for Infinity (no filtering).\",\n            },\n          ],\n      },\n    ],\n  script: dada2_filter_trim.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"
    }
]