CI
93f55cc2ee
Build pipeline: viash-hub.biobox.main-dkgvl
Source commit: ad89f43726
Source message: Add authors to package config and update author information (#180)
* Add authors to package config and update author information
* update changelog
* add linkedin
204 lines
8.4 KiB
JSON
204 lines
8.4 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "bbmap_bbsplit",
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"description": "Split sequencing reads by mapping them to multiple references simultaneously.",
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"type": "object",
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"$defs": {
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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": "string",
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"description": "Sample ID",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"paired": {
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"type": "boolean",
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"description": "Paired fastq files or not?",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"input": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"format": "path",
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"description": "Input fastq files, either one or two (paired), separated by \";\".",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`, example: `[\"reads.fastq\"]`. "
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},
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"ref": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"format": "path",
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"description": "Reference FASTA files, separated by \";\"",
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"help_text": "Type: `file`, multiple: `True`, direction: `input`. "
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},
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"only_build_index": {
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"type": "boolean",
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"description": "If set, only builds the index",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"build": {
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"type": "string",
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"format": "path",
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"description": "Index to be used for mapping",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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},
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"qin": {
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"type": "string",
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"description": "Set to 33 or 64 to specify input quality value ASCII offset",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"interleaved": {
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"type": "boolean",
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"description": "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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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"maxindel": {
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"type": "integer",
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"description": "Don't look for indels longer than this",
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"help_text": "Type: `integer`, multiple: `False`, example: `20`. "
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},
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"minratio": {
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"type": "number",
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"description": "Fraction of max alignment score required to keep a site",
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"help_text": "Type: `double`, multiple: `False`, example: `0.56`. "
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},
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"minhits": {
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"type": "integer",
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"description": "Minimum number of seed hits required for candidate sites",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"ambiguous": {
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"type": "string",
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"description": "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",
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"help_text": "Type: `string`, multiple: `False`, example: `\"best\"`, choices: ``best`, `toss`, `random`, `all``. ",
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"enum": [
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"best",
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"toss",
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"random",
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"all"
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]
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},
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"ambiguous2": {
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"type": "string",
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"description": "Set behavior only for reads that map ambiguously to multiple different references.\nNormal 'ambiguous=' 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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"help_text": "Type: `string`, multiple: `False`, example: `\"best\"`, choices: ``best`, `toss`, `all`, `split``. ",
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"enum": [
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"best",
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"toss",
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"all",
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"split"
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]
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},
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"qtrim": {
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"type": "string",
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"description": "Quality-trim ends to Q5 before mapping",
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"help_text": "Type: `string`, multiple: `False`, choices: ``l`, `r`, `lr``. ",
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"enum": [
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"l",
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"r",
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"lr"
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]
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},
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"untrim": {
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"type": "boolean",
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"description": "Undo trimming after mapping",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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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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"index": {
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"type": "string",
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"format": "path",
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"description": "Location to write the index.\n",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.index\"`, direction: `output`, example: `\"BBSplit_index\"`. ",
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"default": "$id.$key.index"
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},
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"fastq_1": {
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"type": "string",
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"format": "path",
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"description": "Output file for read 1.\n",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fastq_1.fastq\"`, direction: `output`, example: `\"read_out1.fastq\"`. ",
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"default": "$id.$key.fastq_1.fastq"
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},
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"fastq_2": {
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"type": "string",
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"format": "path",
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"description": "Output file for read 2.\n",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.fastq_2.fastq\"`, direction: `output`, example: `\"read_out2.fastq\"`. ",
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"default": "$id.$key.fastq_2.fastq"
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},
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"sam2bam": {
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"type": "string",
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"format": "path",
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"description": "Write a shell script to 'file' that will turn the sam output into a sorted, indexed bam file.\n",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.sam2bam.sh\"`, direction: `output`, example: `\"script.sh\"`. ",
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"default": "$id.$key.sam2bam.sh"
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},
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"scafstats": {
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"type": "string",
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"format": "path",
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"description": "Write statistics on how many reads mapped to which scaffold to this file.\n",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.scafstats.txt\"`, direction: `output`, example: `\"scaffold_stats.txt\"`. ",
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"default": "$id.$key.scafstats.txt"
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},
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"refstats": {
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"type": "string",
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"format": "path",
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"description": "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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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.refstats.txt\"`, direction: `output`, example: `\"reference_stats.txt\"`. ",
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"default": "$id.$key.refstats.txt"
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},
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"nzo": {
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"type": "boolean",
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"description": "Only print lines with nonzero coverage.",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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},
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"bbmap_args": {
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"type": "string",
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"description": "Additional arguments from BBMap to pass to BBSplit.\n",
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"help_text": "Type: `string`, multiple: `False`. "
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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": "string",
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"description": "Path to an output directory.",
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"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
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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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"$ref": "#/$defs/input"
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},
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{
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"$ref": "#/$defs/output"
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},
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{
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"$ref": "#/$defs/nextflow input-output arguments"
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}
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]
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}
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