CI
ad5d79dd3f
Build pipeline: viash-hub.rnaseq.align-quant-r9d67
Source commit: 084cd7d551
Source message: Tidy alignment_quanitification diagram
116 lines
4.2 KiB
JSON
116 lines
4.2 KiB
JSON
{
|
|
"$schema": "https://json-schema.org/draft/2020-12/schema",
|
|
"title": "alignment_quantification",
|
|
"description": "Align reads to the genome using STAR and quantify gene expression using\nSalmon\n",
|
|
"type": "object",
|
|
"$defs": {
|
|
"inputs": {
|
|
"title": "Inputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"input_r1": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"exists": true,
|
|
"description": "FASTQ file containing read 1",
|
|
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
|
|
},
|
|
"input_r2": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"exists": true,
|
|
"description": "FASTQ file containing read 2",
|
|
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
|
|
},
|
|
"input_transcript_fasta": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"exists": true,
|
|
"description": "FASTA file containing transcript sequences",
|
|
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
|
|
},
|
|
"input_gtf": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"exists": true,
|
|
"description": "GTF file containing sequence annotations",
|
|
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
|
|
},
|
|
"input_star_genome_dir": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"exists": true,
|
|
"description": "STAR genome index directory",
|
|
"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
|
|
}
|
|
}
|
|
},
|
|
"outputs": {
|
|
"title": "Outputs",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
"output_star_bam_genome": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "BAM file containing reads aligned to the genome using STAR",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"star/aligned_genome.bam\"`, direction: `output`. ",
|
|
"default": "star/aligned_genome.bam"
|
|
},
|
|
"output_star_bam_transcriptome": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "BAM file containing reads aligned to the transcriptome using STAR",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"star/aligned_transcriptome.bam\"`, direction: `output`. ",
|
|
"default": "star/aligned_transcriptome.bam"
|
|
},
|
|
"output_star_junctions": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "Tabular file containing splice junctions identified by STAR",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"star/splice_junctions.tab\"`, direction: `output`. ",
|
|
"default": "star/splice_junctions.tab"
|
|
},
|
|
"output_star_log": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "STAR execution log file",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"star/log.out\"`, direction: `output`. ",
|
|
"default": "star/log.out"
|
|
},
|
|
"output_salmon": {
|
|
"type": "string",
|
|
"format": "path",
|
|
"description": "salmon alignment mode quantification output directory",
|
|
"help_text": "Type: `file`, multiple: `False`, default: `\"salmon\"`, direction: `output`. ",
|
|
"default": "salmon"
|
|
}
|
|
}
|
|
},
|
|
"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"
|
|
}
|
|
]
|
|
}
|