Build branch main with version main (219bd58)
Build pipeline: viash-hub.demultiplex.main-ks4jt
Source commit: 219bd5816e
Source message: Allow 'Undetermined' samples to be empty. (#50)
This commit is contained in:
@@ -1,179 +1,118 @@
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{
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"$schema": "http://json-schema.org/draft-07/schema",
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"title": "publish",
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"description": "Publish the processed results of the run",
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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. Directory to write fastq data to",
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"help_text": "Type: `file`, required. Directory to write fastq data to"
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}
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,
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"input_falco": {
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"type":
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"string",
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"description": "Type: List of `file`, required, multiple_sep: `\";\"`. Directory to write falco output to",
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"help_text": "Type: List of `file`, required, multiple_sep: `\";\"`. Directory to write falco output to"
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}
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,
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"input_multiqc": {
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"type":
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"string",
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"description": "Type: `file`, required. Location where to write the MultiQC report to",
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"help_text": "Type: `file`, required. Location where to write the MultiQC report to."
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}
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,
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"input_run_information": {
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"type":
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"string",
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"description": "Type: `file`, required. Location where to write the run information to",
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"help_text": "Type: `file`, required. Location where to write the run information to."
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}
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,
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"input_demultiplexer_logs": {
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"type":
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"string",
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"description": "Type: `file`, required. ",
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"help_text": "Type: `file`, required. "
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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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"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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"output_falco": {
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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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"output_multiqc": {
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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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"output_run_information": {
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"type":
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"string",
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"description": "Type: `file`, default: `run_information.csv`. ",
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"help_text": "Type: `file`, default: `run_information.csv`. "
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,
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"default":"run_information.csv"
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}
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,
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"output_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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"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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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "publish",
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"description": "Publish the processed results of the run",
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"type": "object",
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"$defs": {
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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": "string",
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"format": "path",
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"exists": true,
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"description": "Directory to write fastq data to",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"input_falco": {
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"type": "array",
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"items": {
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"type": "string"
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},
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"format": "path",
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"exists": true,
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"description": "Directory to write falco output to",
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"help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
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},
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"input_multiqc": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Location where to write the MultiQC report to.",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"input_run_information": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Location where to write the run information to.",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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},
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"input_demultiplexer_logs": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
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}
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}
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},
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{
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"$ref": "#/definitions/output arguments"
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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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"output": {
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"type": "string",
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"format": "path",
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, default: `\"fastq\"`, direction: `output`. ",
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"default": "fastq"
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},
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"output_falco": {
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"type": "string",
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"format": "path",
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, default: `\"qc/fastqc\"`, direction: `output`. ",
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"default": "qc/fastqc"
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},
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"output_multiqc": {
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"type": "string",
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"format": "path",
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, default: `\"qc/multiqc_report.html\"`, direction: `output`. ",
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"default": "qc/multiqc_report.html"
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},
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"output_run_information": {
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"type": "string",
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"format": "path",
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, default: `\"run_information.csv\"`, direction: `output`. ",
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"default": "run_information.csv"
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},
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"output_demultiplexer_logs": {
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"type": "string",
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"format": "path",
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"description": "",
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"help_text": "Type: `file`, multiple: `False`, default: `\"demultiplexer_logs\"`, direction: `output`. ",
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"default": "demultiplexer_logs"
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}
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}
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},
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{
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"$ref": "#/definitions/nextflow input-output arguments"
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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": "string",
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"description": "Path to an output directory.",
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"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
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}
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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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"$ref": "#/$defs/input arguments"
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},
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{
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"$ref": "#/$defs/output arguments"
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},
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{
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"$ref": "#/$defs/nextflow input-output arguments"
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}
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]
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}
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