CI
93f55cc2ee
Build pipeline: viash-hub.biobox.main-dkgvl
Source commit: ad89f43726
Source message: Add authors to package config and update author information (#180)
* Add authors to package config and update author information
* update changelog
* add linkedin
206 lines
8.4 KiB
JSON
206 lines
8.4 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "bcl_convert",
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"description": "Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n",
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"type": "object",
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"$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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"bcl_input_directory": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "Input run directory",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"bcl_dir\"`. "
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},
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"sample_sheet": {
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"type": "string",
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"format": "path",
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"description": "Path to SampleSheet.csv file (default searched for in --bcl_input_directory)",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"bcl_dir/sample_sheet.csv\"`. "
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},
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"run_info": {
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"type": "string",
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"format": "path",
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"description": "Path to RunInfo.xml file (default root of BCL input directory)",
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"help_text": "Type: `file`, multiple: `False`, direction: `input`, example: `\"bcl_dir/RunInfo.xml\"`. "
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}
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}
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},
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"lane and tile settings": {
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"title": "Lane and tile settings",
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"type": "object",
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"description": "No description",
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"properties": {
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"bcl_only_lane": {
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"type": "integer",
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"description": "Convert only specified lane number (default all lanes)",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"first_tile_only": {
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"type": "boolean",
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"description": "Only convert first tile of input (for testing & debugging)",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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},
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"tiles": {
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"type": "string",
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"description": "Process only a subset of tiles by a regular expression",
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"help_text": "Type: `string`, multiple: `False`, example: `\"s_[0-9]+_1\"`. "
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},
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"exclude_tiles": {
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"type": "string",
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"description": "Exclude set of tiles by a regular expression",
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"help_text": "Type: `string`, multiple: `False`, example: `\"s_[0-9]+_1\"`. "
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}
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}
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},
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"resource arguments": {
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"title": "Resource arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"shared_thread_odirect_output": {
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"type": "boolean",
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"description": "Use linux native asynchronous io (io_submit) for file output (Default=false)",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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},
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"bcl_num_parallel_tiles": {
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"type": "integer",
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"description": "\\# of tiles to process in parallel (default 1)",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"bcl_num_conversion_threads": {
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"type": "integer",
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"description": "\\# of threads for conversion (per tile, default # cpu threads)",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"bcl_num_compression_threads": {
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"type": "integer",
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"description": "\\# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"bcl_num_decompression_threads": {
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"type": "integer",
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"description": "\\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8)",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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}
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}
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},
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"run arguments": {
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"title": "Run arguments",
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"type": "object",
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"description": "No description",
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"properties": {
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"bcl_only_matched_reads": {
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"type": "boolean",
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"description": "For pure BCL conversion, do not output files for 'Undetermined' [unmatched] reads (output by default)",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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},
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"no_lane_splitting": {
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"type": "boolean",
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"description": "Do not split FASTQ file by lane (false by default)",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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},
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"num_unknown_barcodes_reported": {
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"type": "integer",
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"description": "\\# of Top Unknown Barcodes to output (1000 by default)",
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"help_text": "Type: `integer`, multiple: `False`, example: `1000`. "
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},
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"bcl_validate_sample_sheet_only": {
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"type": "boolean",
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"description": "Only validate RunInfo.xml & SampleSheet files (produce no FASTQ files)",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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},
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"strict_mode": {
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"type": "boolean",
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"description": "Abort if any files are missing (false by default)",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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},
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"sample_name_column_enabled": {
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"type": "boolean",
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"description": "Use sample sheet 'Sample_Name' column when naming fastq files & subdirectories",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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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_directory": {
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"type": "string",
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"format": "path",
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"description": "Output directory containig fastq files",
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"help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output_directory\"`, direction: `output`, example: `\"fastq_dir\"`. ",
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"default": "$id.$key.output_directory"
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},
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"bcl_sampleproject_subdirectories": {
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"type": "boolean",
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"description": "Output to subdirectories based upon sample sheet 'Sample_Project' column",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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},
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"fastq_gzip_compression_level": {
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"type": "integer",
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"description": "Set fastq output compression level 0-9 (default 1)",
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"help_text": "Type: `integer`, multiple: `False`, example: `1`. "
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},
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"reports": {
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"type": "string",
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"format": "path",
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"description": "Reports directory",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.reports\"`, direction: `output`, example: `\"reports_dir\"`. ",
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"default": "$id.$key.reports"
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},
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"logs": {
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"type": "string",
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"format": "path",
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"description": "Reports directory",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.logs\"`, direction: `output`, example: `\"logs_dir\"`. ",
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"default": "$id.$key.logs"
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},
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"force": {
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"type": "boolean",
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"description": "Allow destination directory to already exist and overwrite files.\n",
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"help_text": "Type: `boolean`, multiple: `False`, example: `true`. "
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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": "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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"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/lane and tile settings"
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},
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{
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"$ref": "#/$defs/resource arguments"
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},
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{
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"$ref": "#/$defs/run 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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