CI
ef4cabdcee
Build pipeline: viash-hub.htrnaseq.main-fmznz
Source commit: a3b7ae3f31
Source message: update biobox and craftbox versions (#60)
* update biobox and craftbox versions
* update changelog
149 lines
4.6 KiB
JSON
149 lines
4.6 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "runner",
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"description": "Runner for HT RNA-seq pipeline",
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"type": "object",
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"$defs": {
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"input arguments": {
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"title": "Input arguments",
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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": "Base directory of the form `s3:/<bucket>/Sequencing/<Sequencer>/<RunID>/<demultiplex_dir>`",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"barcodesFasta": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"genomeDir": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"annotation": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"ignore": {
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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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"description": "Pool names to ignore.",
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"help_text": "Type: `string`, multiple: `True`, default: `[\"Undetermined\"]`. ",
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"default": [
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"Undetermined"
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]
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},
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"umi_length": {
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"type": "integer",
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"description": "Length of the UMI sequences\n",
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"help_text": "Type: `integer`, multiple: `False`, default: `10`. ",
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"default": 10
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},
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"run_params": {
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"type": "string",
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"format": "path",
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, default: `\"params.yaml\"`, direction: `output`. ",
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"default": "params.yaml"
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}
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}
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},
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"metadata arguments": {
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"title": "Metadata 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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"project_id": {
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"type": "string",
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"description": "Project ID",
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"help_text": "Type: `string`, multiple: `False`, required. "
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},
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"experiment_id": {
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"type": "string",
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"description": "Experiment ID",
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"help_text": "Type: `string`, multiple: `False`, required. "
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}
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}
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},
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"annotation flags": {
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"title": "Annotation flags",
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"type": "object",
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"description": "No description",
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"properties": {
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"plain_output": {
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"type": "boolean",
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"description": "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\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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"publish arguments": {
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"title": "Publish arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"fastq_publish_dir": {
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"type": "string",
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"description": "",
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"help_text": "Type: `string`, multiple: `False`, required. "
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},
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"results_publish_dir": {
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"type": "string",
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"description": "",
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"help_text": "Type: `string`, multiple: `False`, required. "
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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": "#/$defs/input arguments"
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},
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{
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"$ref": "#/$defs/metadata arguments"
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},
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{
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"$ref": "#/$defs/annotation flags"
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},
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{
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"$ref": "#/$defs/publish arguments"
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},
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{
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"$ref": "#/$defs/nextflow input-output arguments"
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}
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]
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}
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