CI
b720ad07f9
Build pipeline: viash-hub.demultiplex.main-p5t6v
Source commit: f591b7849f
Source message: Output demultiplexer log files (#41)
201 lines
7.7 KiB
JSON
201 lines
7.7 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 canonical form `s3://\u003cbucket\u003e/\u003cpath\u003e/\u003cRunID\u003e/`",
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"help_text": "Type: `file`, required. Base directory of the canonical form `s3://\u003cbucket\u003e/\u003cpath\u003e/\u003cRunID\u003e/`.\nA tarball (tar.gz, .tgz, .tar) containing run information can be provided in which\ncase the RunID is set to the name of the tarball without the extension.\n"
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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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"plain_output": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/\u003cdate_time\u003e_demultiplex_\u003cversion\u003e/",
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"help_text": "Type: `boolean_true`, default: `false`. Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/\u003cdate_time\u003e_demultiplex_\u003cversion\u003e/.\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: `fastq`. ",
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"help_text": "Type: `file`, default: `fastq`. "
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,
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"default":"fastq"
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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: `qc/fastqc`. ",
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"help_text": "Type: `file`, default: `qc/fastqc`. "
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,
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"default":"qc/fastqc"
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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: `qc/multiqc_report.html`. ",
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"help_text": "Type: `file`, default: `qc/multiqc_report.html`. "
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,
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"default":"qc/multiqc_report.html"
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}
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,
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"demultiplexer_logs": {
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"type":
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"string",
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"description": "Type: `file`, default: `demultiplexer_logs`. ",
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"help_text": "Type: `file`, default: `demultiplexer_logs`. "
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,
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"default":"demultiplexer_logs"
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}
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}
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},
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"other arguments" : {
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"title": "Other arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"skip_copycomplete_check": {
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"type":
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"boolean",
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"description": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete",
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"help_text": "Type: `boolean_true`, default: `false`. Disable the check for the presence of a \"CopyComplete.txt\" file in input\ndirectory in case of Illumina data.\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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"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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"$ref": "#/definitions/other arguments"
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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}
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]
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}
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