CI
04a5851ff8
Build pipeline: viash-hub.biobox.main-tb4cv
Source commit: 7158daa5f6
Source message: Fix bases2fastq component, update to latest practices (#190)
* wip updates
* refactor component
* assume bases2fastq follows semver
* fix version command
* add entry to changelog
* move to minor changes
83 lines
3.5 KiB
JSON
83 lines
3.5 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "bedtools_complement",
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"description": "Find genomic intervals that are NOT covered by input intervals.\n\nThis tool returns the complement of genomic intervals - the regions\nof the genome that are NOT covered by the input features. Useful for\nfinding gaps, uncovered regions, or background intervals.\n",
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"type": "object",
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"$defs": {
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"inputs": {
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"title": "Inputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"input": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Input file in BED, GFF, or VCF format.\n\n**BED format:** Standard genomic interval format\n**GFF format:** Gene feature format with annotations\n**VCF format:** Variant call format\n**Requirements:** Should be sorted by chromosome and position for optimal performance\n",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"covered_regions.bed\"`. "
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},
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"genome": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Genome file defining chromosome names and sizes.\n\n**Format:** Tab-delimited file with chromosome name and size\n**Example line:** chr1 249250621\n**Sources:** Can be created with samtools faidx or UCSC Table Browser\n**Purpose:** Defines the complete genomic space for complement calculation\n",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"genome.txt\"`. "
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}
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}
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},
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"outputs": {
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"title": "Outputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type": "string",
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"format": "path",
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"description": "Output file with complement intervals.\n\nContains genomic intervals representing the regions NOT covered\nby the input intervals",
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"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.bed\"`, direction: `output`, example: `\"uncovered_regions.bed\"`. ",
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"default": "$id.$key.output.bed"
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}
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}
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},
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"options": {
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"title": "Options",
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"type": "object",
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"description": "No description",
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"properties": {
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"limit_chromosomes": {
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"type": "boolean",
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"description": "Limit output to chromosomes present in input file.\n\n**Default:** Output includes all chromosomes from genome file\n**When enabled:** Only output complement for chromosomes that have\nrecords in the input file\n**Use case:** Focus analysis on chromosomes of interest\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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}
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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/inputs"
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},
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{
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"$ref": "#/$defs/outputs"
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},
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{
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"$ref": "#/$defs/options"
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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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