{ "$schema": "http://json-schema.org/draft-07/schema", "title": "bbmap_bbsplit", "description": "Split sequencing reads by mapping them to multiple references simultaneously.", "type": "object", "definitions": { "input" : { "title": "Input", "type": "object", "description": "No description", "properties": { "id": { "type": "string", "description": "Type: `string`. Sample ID", "help_text": "Type: `string`. Sample ID" } , "paired": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. Paired fastq files or not?", "help_text": "Type: `boolean_true`, default: `false`. Paired fastq files or not?" , "default": "False" } , "input": { "type": "string", "description": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"", "help_text": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"." } , "ref": { "type": "string", "description": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\"", "help_text": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\". The primary reference should be specified first." } , "only_build_index": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. If set, only builds the index", "help_text": "Type: `boolean_true`, default: `false`. If set, only builds the index. Otherwise, mapping is performed." , "default": "False" } , "build": { "type": "string", "description": "Type: `file`. Index to be used for mapping", "help_text": "Type: `file`. Index to be used for mapping. \n" } , "qin": { "type": "string", "description": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset", "help_text": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset. Automatically detected if\nnot specified.\n" } , "interleaved": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping", "help_text": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n" , "default": "False" } , "maxindel": { "type": "integer", "description": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this", "help_text": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this. Lower is faster. Set to \u003e=100k for RNA-seq.\n" } , "minratio": { "type": "number", "description": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site", "help_text": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site. Higher is faster.\n" } , "minhits": { "type": "integer", "description": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites", "help_text": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites. Higher is faster.\n" } , "ambiguous": { "type": "string", "description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations)", "help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations).\n * best Use the first best site (Default)\n * toss Consider unmapped\n * random Select one top-scoring site randomly\n * all Retain all top-scoring sites. Does not work yet with SAM output\n", "enum": ["best", "toss", "random", "all"] } , "ambiguous2": { "type": "string", "description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references", "help_text": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references.\nNormal \u0027ambiguous=\u0027 controls behavior on all ambiguous reads;\nAmbiguous2 excludes reads that map ambiguously within a single reference.\n * best Use the first best site (Default)\n * toss Consider unmapped\n * all Write a copy to the output for each reference to which it maps\n * split Write a copy to the AMBIGUOUS_ output for each reference to which it maps\n", "enum": ["best", "toss", "all", "split"] } , "qtrim": { "type": "string", "description": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping", "help_text": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping. Options are \u0027l\u0027 (left), \u0027r\u0027 (right), and \u0027lr\u0027 (both).\n", "enum": ["l", "r", "lr"] } , "untrim": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. Undo trimming after mapping", "help_text": "Type: `boolean_true`, default: `false`. Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings." , "default": "False" } } }, "output" : { "title": "Output", "type": "object", "description": "No description", "properties": { "index": { "type": "string", "description": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index", "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index.\n" , "default": "$id.$key.index.index" } , "fastq_1": { "type": "string", "description": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1", "help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1.\n" , "default": "$id.$key.fastq_1.fastq" } , "fastq_2": { "type": "string", "description": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2", "help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2.\n" , "default": "$id.$key.fastq_2.fastq" } , "sam2bam": { "type": "string", "description": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file", "help_text": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file.\n" , "default": "$id.$key.sam2bam.sh" } , "scafstats": { "type": "string", "description": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file", "help_text": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file.\n" , "default": "$id.$key.scafstats.txt" } , "refstats": { "type": "string", "description": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file", "help_text": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n" , "default": "$id.$key.refstats.txt" } , "nzo": { "type": "boolean", "description": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage", "help_text": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage." , "default": "False" } , "bbmap_args": { "type": "string", "description": "Type: `string`. Additional arguments from BBMap to pass to BBSplit", "help_text": "Type: `string`. Additional arguments from BBMap to pass to BBSplit.\n" } } }, "nextflow input-output arguments" : { "title": "Nextflow input-output arguments", "type": "object", "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.", "properties": { "publish_dir": { "type": "string", "description": "Type: `string`, required, example: `output/`. Path to an output directory", "help_text": "Type: `string`, required, example: `output/`. Path to an output directory." } , "param_list": { "type": "string", "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel", "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.", "hidden": true } } } }, "allOf": [ { "$ref": "#/definitions/input" }, { "$ref": "#/definitions/output" }, { "$ref": "#/definitions/nextflow input-output arguments" } ] }