CI
9405bcedbe
Build pipeline: viash-hub.rnaseq.reporting-bsrzh
Source commit: 6343c3cfef
Source message: add toolbox, update craftbox
79 lines
2.7 KiB
JSON
79 lines
2.7 KiB
JSON
{
|
|
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
|
"title": "prepare_genome",
|
|
"description": "Prepare genome and transcriptome FASTA files for STAR alignment by adding\nnecessary headers and creating a STAR index.\n",
|
|
"type": "object",
|
|
"$defs": {
|
|
"inputs": {
|
|
"title": "Inputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"input_genome_fasta": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "",
|
|
"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genome.fasta.gz\"`. "
|
|
},
|
|
"input_transcriptome_gtf": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "",
|
|
"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"genes.gtf.gz\"`. "
|
|
}
|
|
}
|
|
},
|
|
"outputs": {
|
|
"title": "Outputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"output_genome_fasta": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_genome_fasta.fasta\"`, direction: `output`, example: `\"genome.fasta\"`. ",
|
|
"default": "$id.$key.output_genome_fasta.fasta"
|
|
},
|
|
"output_transcriptome_gtf": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_transcriptome_gtf.gtf\"`, direction: `output`, example: `\"transcriptome.gtf\"`. ",
|
|
"default": "$id.$key.output_transcriptome_gtf.gtf"
|
|
},
|
|
"output_star_index": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output_star_index\"`, direction: `output`. ",
|
|
"default": "$id.$key.output_star_index"
|
|
}
|
|
}
|
|
},
|
|
"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/inputs"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/outputs"
|
|
},
|
|
{
|
|
"$ref": "#/$defs/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|