311 lines
13 KiB
JSON
311 lines
13 KiB
JSON
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{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "bbmap_bbsplit",
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"description": "Split sequencing reads by mapping them to multiple references simultaneously.",
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"type": "object",
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"definitions": {
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"input" : {
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"title": "Input",
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"type": "object",
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"description": "No description",
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"properties": {
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"id": {
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"type":
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"string",
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"description": "Type: `string`. Sample ID",
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"help_text": "Type: `string`. Sample ID"
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}
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,
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"paired": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Paired fastq files or not?",
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"help_text": "Type: `boolean_true`, default: `false`. Paired fastq files or not?"
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,
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"default": "False"
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}
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,
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"input": {
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"type":
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"string",
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"description": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"",
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"help_text": "Type: List of `file`, example: `reads.fastq`, multiple_sep: `\";\"`. Input fastq files, either one or two (paired), separated by \";\"."
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}
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,
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"ref": {
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"type":
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"string",
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"description": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\"",
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"help_text": "Type: List of `file`, multiple_sep: `\";\"`. Reference FASTA files, separated by \";\". The primary reference should be specified first."
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}
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,
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"only_build_index": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. If set, only builds the index",
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"help_text": "Type: `boolean_true`, default: `false`. If set, only builds the index. Otherwise, mapping is performed."
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,
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"default": "False"
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}
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,
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"build": {
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"type":
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"string",
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"description": "Type: `string`, example: `1`. Designate index to use",
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"help_text": "Type: `string`, example: `1`. Designate index to use. Corresponds to the number specified when building the index.\nIf building the index, this will be the build\u0027s id. If multiple references are indexed\nin the same directory, each needs a unique build ID. Default: 1.\n"
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}
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,
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"qin": {
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"type":
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"string",
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"description": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset",
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"help_text": "Type: `string`. Set to 33 or 64 to specify input quality value ASCII offset. Automatically detected if\nnot specified.\n"
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}
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,
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"interleaved": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping",
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"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"
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,
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"default": "False"
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}
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,
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"maxindel": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `20`. Don\u0027t look for indels longer than this",
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"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"
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}
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,
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"minratio": {
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"type":
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"number",
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"description": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site",
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"help_text": "Type: `double`, example: `0.56`. Fraction of max alignment score required to keep a site. Higher is faster.\n"
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}
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,
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"minhits": {
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"type":
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"integer",
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"description": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites",
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"help_text": "Type: `integer`, example: `1`. Minimum number of seed hits required for candidate sites. Higher is faster.\n"
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}
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,
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"ambiguous": {
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"type":
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"string",
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"description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `random`, `all``. Set behavior on ambiguously-mapped reads (with multiple top-scoring mapping locations)",
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"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",
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"enum": ["best", "toss", "random", "all"]
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}
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,
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"ambiguous2": {
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"type":
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"string",
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"description": "Type: `string`, example: `best`, choices: ``best`, `toss`, `all`, `split``. Set behavior only for reads that map ambiguously to multiple different references",
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"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",
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"enum": ["best", "toss", "all", "split"]
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}
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,
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"qtrim": {
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"type":
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"string",
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"description": "Type: `string`, choices: ``l`, `r`, `lr``. Quality-trim ends to Q5 before mapping",
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"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",
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"enum": ["l", "r", "lr"]
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}
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,
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"untrim": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Undo trimming after mapping",
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"help_text": "Type: `boolean_true`, default: `false`. Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings."
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,
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"default": "False"
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}
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}
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},
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"output" : {
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"title": "Output",
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"type": "object",
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"description": "No description",
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"properties": {
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"fastq_1": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1",
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"help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1.\n"
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"default": "$id.$key.fastq_1.fastq"
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}
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,
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"fastq_2": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2",
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"help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2.\n"
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,
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"default": "$id.$key.fastq_2.fastq"
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}
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,
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"sam2bam": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file",
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"help_text": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file.\n"
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,
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"default": "$id.$key.sam2bam.sh"
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}
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,
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"scafstats": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file",
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"help_text": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file.\n"
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,
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"default": "$id.$key.scafstats.txt"
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}
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,
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"refstats": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file",
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"help_text": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n"
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,
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"default": "$id.$key.refstats.txt"
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}
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,
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"nzo": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage",
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"help_text": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage."
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,
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"default": "False"
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}
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,
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"bbmap_args": {
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"type":
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"string",
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"description": "Type: `string`. Additional arguments from BBMap to pass to BBSplit",
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"help_text": "Type: `string`. Additional arguments from BBMap to pass to BBSplit.\n"
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}
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}
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},
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"nextflow input-output arguments" : {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"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.",
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"properties": {
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"publish_dir": {
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"type":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"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.",
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"hidden": true
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/input"
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},
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{
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"$ref": "#/definitions/output"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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