CI
50ab36217a
Build pipeline: viash-hub.demultiplex.main-wxzkf
Source commit: 6e71519815
Source message: Replace Falco with FastQC (#51)
129 lines
4.5 KiB
JSON
129 lines
4.5 KiB
JSON
{
|
|
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
|
"title": "demultiplex",
|
|
"description": "Demultiplexing of raw sequencing data",
|
|
"type": "object",
|
|
"$defs": {
|
|
"input arguments": {
|
|
"title": "Input arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"id": {
|
|
"type": "string",
|
|
"description": "Unique identifier for the run",
|
|
"help_text": "Type: `string`, multiple: `False`. "
|
|
},
|
|
"input": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"exists": true,
|
|
"description": "Directory containing raw sequencing data",
|
|
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
|
|
},
|
|
"run_information": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "CSV file containing sample information, which will be used as \ninput for the demultiplexer",
|
|
"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
|
|
},
|
|
"demultiplexer": {
|
|
"type": "string",
|
|
"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",
|
|
"help_text": "Type: `string`, multiple: `False`, choices: ``bases2fastq`, `bclconvert``. ",
|
|
"enum": [
|
|
"bases2fastq",
|
|
"bclconvert"
|
|
]
|
|
}
|
|
}
|
|
},
|
|
"output arguments": {
|
|
"title": "Output arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"output": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "Directory to write fastq data to",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id/fastq\"`, direction: `output`. ",
|
|
"default": "$id/fastq"
|
|
},
|
|
"output_sample_qc": {
|
|
"type": "array",
|
|
"items": {
|
|
"type": "string"
|
|
},
|
|
"format": "path",
|
|
"description": "Directory to write FastQC output to",
|
|
"help_text": "Type: `file`, multiple: `True`, default: `[\"$id/qc/fastqc\"]`, direction: `output`. ",
|
|
"default": [
|
|
"$id/qc/fastqc"
|
|
]
|
|
},
|
|
"multiqc_output": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "Location where to write MultiQC output to",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id/qc/multiqc_report.html\"`, direction: `output`. ",
|
|
"default": "$id/qc/multiqc_report.html"
|
|
},
|
|
"output_run_information": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "",
|
|
"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id/run_information.csv\"`, direction: `output`. ",
|
|
"default": "$id/run_information.csv"
|
|
},
|
|
"demultiplexer_logs": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "",
|
|
"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id/demultiplexer_logs\"`, direction: `output`. ",
|
|
"default": "$id/demultiplexer_logs"
|
|
}
|
|
}
|
|
},
|
|
"other arguments": {
|
|
"title": "Other arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"skip_copycomplete_check": {
|
|
"type": "boolean",
|
|
"description": "Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\n",
|
|
"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
|
|
"default": false
|
|
}
|
|
}
|
|
},
|
|
"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": "Path to an output directory.",
|
|
"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
|
|
}
|
|
}
|
|
}
|
|
},
|
|
"allOf": [
|
|
{
|
|
"$ref": "#/$defs/input arguments"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/output arguments"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/other arguments"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|