CI
09a049c60c
Build pipeline: viash-hub.demultiplex.v0.3-jknqb
Source commit: 35e1ab8495
Source message: Bump version to 0.3.1
176 lines
7.0 KiB
JSON
176 lines
7.0 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "runner",
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"description": "Runner for demultiplexing of raw sequencing data",
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"type": "object",
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"definitions": {
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"input arguments" : {
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"title": "Input arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"input": {
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"type":
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"string",
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"description": "Type: `file`, required. Base directory of the form `s3:/\u003cbucket\u003e/Sequencing/\u003cSequencer\u003e/\u003cRunID\u003e/`",
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"help_text": "Type: `file`, required. Base directory of the form `s3:/\u003cbucket\u003e/Sequencing/\u003cSequencer\u003e/\u003cRunID\u003e/`"
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}
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,
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"run_information": {
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"type":
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"string",
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"description": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer",
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"help_text": "Type: `file`. CSV file containing sample information, which will be used as \ninput for the demultiplexer. Canonically called \u0027SampleSheet.csv\u0027 (Illumina)\nor \u0027RunManifest.csv\u0027 (Element Biosciences). If not specified,\nwill try to autodetect the sample sheet in the input directory.\nRequires --demultiplexer to be set.\n"
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}
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,
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"demultiplexer": {
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"type":
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"string",
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"description": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data",
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"help_text": "Type: `string`, choices: ``bases2fastq`, `bclconvert``. Demultiplexer to use, choice depends on the provider\nof the instrument that was used to generate the data.\nWhen not using --sample_sheet, specifying this argument is not\nrequired.\n",
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"enum": ["bases2fastq", "bclconvert"]
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}
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}
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},
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"annotation flags" : {
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"title": "Annotation flags",
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"type": "object",
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"description": "No description",
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"properties": {
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"add_date_time": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Add date and time to the output directory name",
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"help_text": "Type: `boolean_true`, default: `false`. Add date and time to the output directory name. This is useful\nwhen running the same pipeline multiple times on the same input\ndirectory.\n"
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,
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"default":false
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}
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,
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"add_workflow_id": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Add a workflow identifier to the output directory name",
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"help_text": "Type: `boolean_true`, default: `false`. Add a workflow identifier to the output directory name.\n"
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,
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"default":false
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}
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}
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},
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"output arguments" : {
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"title": "Output arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"fastq_output": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.fastq_output.fastq_output`. ",
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"help_text": "Type: `file`, default: `$id.$key.fastq_output.fastq_output`. "
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,
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"default":"$id.$key.fastq_output.fastq_output"
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}
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,
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"falco_output": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.falco_output.falco_output`. ",
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"help_text": "Type: `file`, default: `$id.$key.falco_output.falco_output`. "
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,
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"default":"$id.$key.falco_output.falco_output"
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}
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,
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"multiqc_output": {
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"type":
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"string",
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"description": "Type: `file`, default: `$id.$key.multiqc_output.html`. ",
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"help_text": "Type: `file`, default: `$id.$key.multiqc_output.html`. "
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,
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"default":"$id.$key.multiqc_output.html"
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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":
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"string",
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"description": "Type: `string`, required, example: `output/`. Path to an output directory",
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"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
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}
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,
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"param_list": {
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"type":
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"string",
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"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
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"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.",
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"hidden": true
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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": "#/definitions/input arguments"
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},
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{
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"$ref": "#/definitions/annotation flags"
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},
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{
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"$ref": "#/definitions/output arguments"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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