CI
10ff085552
Build pipeline: viash-hub.demultiplex.main-qzwsk
Source commit: 26bd658d6e
Source message: Add detect_demultiplexer subworkflow (#52)
75 lines
2.8 KiB
JSON
75 lines
2.8 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "detect_demultiplexer",
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"description": "Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n",
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"type": "object",
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"$defs": {
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"arguments": {
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"title": "Arguments",
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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": "Unique identifier for the run",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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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": "Directory containing raw sequencing data",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"run_information": {
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"type": "string",
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"format": "path",
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"description": "CSV file containing sample information, which will be used as \ninput for the demultiplexer",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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},
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"demultiplexer": {
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"type": "string",
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"description": "Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
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"help_text": "Type: `string`, multiple: `False`, choices: ``bases2fastq`, `bclconvert``. ",
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"enum": [
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"bases2fastq",
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"bclconvert"
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]
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},
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"demultiplexer_output": {
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"type": "string",
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"description": "Demultiplexer program",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"run_information_output": {
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"type": "string",
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"format": "path",
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"description": "Sample information that can be used to demultiplex the input data",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_information_output\"`, direction: `output`. ",
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"default": "$id.$key.run_information_output"
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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/arguments"
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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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