CI
14e0d12189
Build pipeline: viash-hub.rnaseq.main-b6jtr
Source commit: ce40a4a6d9
Source message: add unit tests
130 lines
4.8 KiB
JSON
130 lines
4.8 KiB
JSON
{
|
|
"$schema": "http://json-schema.org/draft-07/schema",
|
|
"title": "bedtools_genomecov",
|
|
"description": "Compute BEDGRAPH (-bg) summaries of feature coverage",
|
|
"type": "object",
|
|
"definitions": {
|
|
|
|
|
|
|
|
"input" : {
|
|
"title": "Input",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"strandedness": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, choices: ``unstranded`, `forward`, `reverse`, `auto``. Sample strand-specificity",
|
|
"help_text": "Type: `string`, choices: ``unstranded`, `forward`, `reverse`, `auto``. Sample strand-specificity.",
|
|
"enum": ["unstranded", "forward", "reverse", "auto"]
|
|
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"bam": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`. Genome BAM file",
|
|
"help_text": "Type: `file`. Genome BAM file"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"extra_bedtools_args": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, default: ``. ",
|
|
"help_text": "Type: `string`, default: ``. "
|
|
,
|
|
"default":""
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"output" : {
|
|
"title": "Output",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"bedgraph_forward": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. ",
|
|
"help_text": "Type: `file`, default: `$id.$key.bedgraph_forward.bedgraph`. "
|
|
,
|
|
"default":"$id.$key.bedgraph_forward.bedgraph"
|
|
}
|
|
|
|
|
|
,
|
|
"bedgraph_reverse": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. ",
|
|
"help_text": "Type: `file`, default: `$id.$key.bedgraph_reverse.bedgraph`. "
|
|
,
|
|
"default":"$id.$key.bedgraph_reverse.bedgraph"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"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": "Type: `string`, required, example: `output/`. Path to an output directory",
|
|
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"param_list": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
|
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
|
|
"hidden": true
|
|
|
|
}
|
|
|
|
|
|
}
|
|
}
|
|
},
|
|
"allOf": [
|
|
|
|
{
|
|
"$ref": "#/definitions/input"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/output"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|