"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."
"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."
"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.",
