CI
cd5554d22f
Build pipeline: vsh-ci-build-template-k4qzr
Source commit: 173327cc56
Source message: Cellranger multi conversion: fix combined AB + CB probe experiments (#1062)
75 lines
2.5 KiB
JSON
75 lines
2.5 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "build_star_reference",
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"description": "Create a reference for STAR from a set of fasta files.",
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"type": "object",
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"$defs": {
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"input/output": {
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"title": "Input/Output",
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"type": "object",
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"description": "No description",
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"properties": {
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"genome_fasta": {
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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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"format": "path",
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"exists": true,
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"description": "The fasta files to be included in the reference",
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"help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"chr1.fasta\";\"chr2.fasta\"]`. "
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},
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"transcriptome_gtf": {
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"type": "string",
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"format": "path",
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"description": "Specifies the path to the file with annotated transcripts in the standard GTF\nformat",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`. "
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},
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"output": {
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"type": "string",
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"format": "path",
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"description": "Path to output directory",
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"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`, example: `\"/path/to/foo\"`. ",
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"default": "$id.$key.output"
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}
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}
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},
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"genome indexing arguments": {
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"title": "Genome indexing arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"genomeSAindexNbases": {
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"type": "integer",
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"description": "Length (bases) of the SA pre-indexing string",
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"help_text": "Type: `integer`, multiple: `False`, default: `14`. ",
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"default": 14
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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/output"
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},
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{
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"$ref": "#/$defs/genome indexing 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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