CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
116 lines
4.2 KiB
JSON
116 lines
4.2 KiB
JSON
{
|
|
"$schema": "http://json-schema.org/draft-07/schema",
|
|
"title": "preseq_lcextrap",
|
|
"description": "Computing the expected future yield of distinct reads and bounds on the number of total distinct reads in the library and the associated confidence intervals.",
|
|
"type": "object",
|
|
"definitions": {
|
|
|
|
|
|
|
|
"input" : {
|
|
"title": "Input",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"input": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`. Input genome BAM/BED file",
|
|
"help_text": "Type: `file`. Input genome BAM/BED file"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"extra_preseq_args": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. ",
|
|
"help_text": "Type: `string`. "
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"paired": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean`. Paired-end reads?",
|
|
"help_text": "Type: `boolean`. Paired-end reads?"
|
|
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"output" : {
|
|
"title": "Output",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"output": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, default: `$id.$key.output.txt`. ",
|
|
"help_text": "Type: `file`, default: `$id.$key.output.txt`. "
|
|
,
|
|
"default": "$id.$key.output.txt"
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"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"
|
|
}
|
|
]
|
|
}
|