CI
c27267ad00
Build pipeline: viash-hub.htrnaseq.v0.14.0-pk2tm
Source commit: eeda989650
Source message: Bump version to v0.14.0
187 lines
6.6 KiB
JSON
187 lines
6.6 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>`.\nMust contains FASTQ files in the format `PoolName_S*_L*_R1_001.fastq.gz` where\n * PoolName is a unique ID for the microwell plates or combination thereof.\n * S followed by a running number: the sample number based on the order\n that samples are listed in the sample sheet (that was used to demultiplex the pools)\n starting with 1 (e.g",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"run_id": {
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"type": "string",
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"description": "Unique ID for the sequencing run\n",
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"help_text": "Type: `string`, multiple: `False`. "
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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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"pools": {
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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": "Filter the FASTQ files in the input directory to only include pools from the provided list.\nPool names are inferred from the FASTQ file names (see input argument for more information).\nBy default all pools are included.\n",
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"help_text": "Type: `string`, multiple: `True`. "
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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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}
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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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"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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"output arguments": {
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"title": "Output arguments",
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"type": "object",
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"description": "Parameters that determine the structure of the output. These parameters are provided for internal use only\nand their defaults should not be overwritten.\n",
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"properties": {
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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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"star_output_dir": {
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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: `\"star_output\"`, direction: `output`. ",
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"default": "star_output"
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},
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"nrReadsNrGenesPerChrom_dir": {
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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: `\"nrReadsNrGenesPerChrom\"`, direction: `output`. ",
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"default": "nrReadsNrGenesPerChrom"
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},
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"star_qc_metrics_dir": {
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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: `\"starLogs\"`, direction: `output`. ",
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"default": "starLogs"
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},
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"eset_dir": {
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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: `\"esets\"`, direction: `output`. ",
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"default": "esets"
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},
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"f_data_dir": {
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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: `\"fData\"`, direction: `output`. ",
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"default": "fData"
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},
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"p_data_dir": {
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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: `\"pData\"`, direction: `output`. ",
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"default": "pData"
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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/publish arguments"
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},
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{
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"$ref": "#/$defs/output 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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