75 lines
3.2 KiB
JSON
75 lines
3.2 KiB
JSON
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{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "make_reference",
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"description": "Preprocess and build a transcriptome reference.\n\nExample input files are:\n - `genome_fasta`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz\n - `transcriptome_gtf`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz\n - `ercc`: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\n",
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"type": "object",
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"$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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"genome_fasta": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Reference genome fasta",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"genome_fasta.fa.gz\"`. "
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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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"exists": true,
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"description": "Reference transcriptome annotation.",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"transcriptome.gtf.gz\"`. "
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},
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"ercc": {
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"type": "string",
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"format": "path",
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"description": "ERCC sequence and annotation file.",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"ercc.zip\"`. "
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},
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"subset_regex": {
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"type": "string",
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"description": "Will subset the reference chromosomes using the given regex.",
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"help_text": "Type: `string`, multiple: `False`, example: `\"(ERCC-00002|chr1)\"`. "
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},
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"output_fasta": {
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"type": "string",
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"format": "path",
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"description": "Output genome sequence fasta.",
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"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_fasta.gz\"`, direction: `output`, example: `\"genome_sequence.fa.gz\"`. ",
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"default": "$id.$key.output_fasta.gz"
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},
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"output_gtf": {
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"type": "string",
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"format": "path",
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"description": "Output transcriptome annotation gtf.",
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"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_gtf.gz\"`, direction: `output`, example: `\"transcriptome_annotation.gtf.gz\"`. ",
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"default": "$id.$key.output_gtf.gz"
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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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