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nextflow_schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/ausargph/master/nextflow_schema.json",
"title": "nf-core/ausargph pipeline parameters",
"description": "testing",
"type": "object",
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/ausargph/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
}
}
},
"general_options": {
"title": "Filter genome, Blat Database and general options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome and and Blat Database related files and options required for the workflow.",
"required": ["blat_db"],
"properties": {
"stage": {
"type": "string",
"description": "The stage to start the workflow from ('from-start' or 'from-prg'). By default the workflow runs 'from-start' meaning it looks for a sample info file with paths to raw reads. If '--stage from-prg' is specified the workflow looks for a modified sample info file with paths to PRG files.",
"help_text": ".",
"fa_icon": "fas fa-question-circle",
"default": "from-start",
"enum": ["from-start", "from-prg", "end-prg"]
},
"filter": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to the filter sequences FASTA file.",
"help_text": "The filtering sequences file is just another FASTA file of your focal loci, but from phylogenetically near samples (high similarity, e.g. intra-family). This is optional, but may be useful for speeding up the assembly step. These sequences are used as a reference to quickly (and loosely) map the raw reads against to exclude off-target sequences that would otherwise slow down the assembly. Locus names do not have to be unique and redundant targets from different taxa may improve filtration.",
"fa_icon": "fas fa-dna"
},
"blat_db": {
"type": "string",
"format": "file-path",
"description": "Path to the target sequences FASTA file.",
"help_text": "The target sequence file is simply a FASTA file of your focal loci. Locus names must be unique, and ideally the target sequence data is not too divergent from your samples (though BLAT is quite flexible). An example targets file is included in bin/SqCL_Targets.fasta, and is appropriate for use with SqCL projects.",
"fa_icon": "fa fa-database"
},
"tree_method": {
"type": "string",
"description": "the supported options are: 'iqtree' or 'raxml'.",
"help_text": "Choose the preferred tree estimation method for individual locus trees. All methods should provide qualitatively identical results. Suggested Usage: iqtree",
"default": "iqtree",
"fa_icon": "fas fa-question-circle",
"enum": ["iqtree", "raxml"]
},
"assembly": {
"type": "string",
"description": "The assembly to be used in the analysis.",
"help_text": "Supported options are: 'trinity' or 'SPAdes'. Suggested Usage: trinity",
"default": "trinity",
"fa_icon": "fas fa-question-circle",
"enum": ["trinity", "SPAdes"]
},
"trim_alignment": {
"type": "boolean",
"description": "Trim initial MAFFT alignments.",
"help_text": "if true, use GBLOCKS to trim initial MAFFT alignments. May proceed slowly. If false, proceed to phylogenetic estimation using initial MAFFT alignments",
"default": false,
"fa_icon": "fas fa-question-circle"
},
"disable_adapter_trimming": {
"type": "boolean",
"description": "Disable trimming adapter in the input reads.",
"help_text": "if true, ...... ",
"default": false,
"fa_icon": "fas fa-question-circle"
},
"batching_size": {
"type": "integer",
"description": "Number of alignment files to be processed sequentially in batches to avoide submitting large number of jobs when using HPCs.",
"help_text": "Number of sample files that constitute a batch. Controls the number of output files generated which is sometimes limited on HPCs (1 million), see [here](https://groups.google.com/g/trinityrnaseq-users/c/w9S8UwL8uiU/m/KzdBydHp7RsJ). This helps to avoid generating large number of files as well as to reduce the number of the submitted jobs to an HPC.",
"default": 250,
"fa_icon": "fas fa-question-circle"
},
"trinity_scratch_tmp": {
"type": "boolean",
"description": "Trinity generates large number of intermediate files which can be an issue for some HPCs that limits the file number for each user. This option will make trinity writes to `/tmp` directory on the compute node then copy the compressed output directory (not the fasta) to the workdirectory to avoid this issue.",
"default": true,
"fa_icon": "fas fa-question-circle"
},
"no_tree_merge": {
"type": "boolean",
"description": "Do not merge all trees at the end.",
"default": false,
"fa_icon": "fas fa-question-circle"
}
}
},
"institutional_config_options": {
"title": "Institutional config options",
"type": "object",
"fa_icon": "fas fa-university",
"description": "Parameters used to describe centralised config profiles. These should not be edited.",
"help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.",
"properties": {
"custom_config_version": {
"type": "string",
"description": "Git commit id for Institutional configs.",
"default": "master",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"custom_config_base": {
"type": "string",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
"help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.",
"fa_icon": "fas fa-users-cog"
},
"config_profile_name": {
"type": "string",
"description": "Institutional config name.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_description": {
"type": "string",
"description": "Institutional config description.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_contact": {
"type": "string",
"description": "Institutional config contact information.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"config_profile_url": {
"type": "string",
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
}
}
},
"max_job_request_options": {
"title": "Max job request options",
"type": "object",
"fa_icon": "fab fa-acquisitions-incorporated",
"description": "Set the top limit for requested resources for any single job.",
"help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.",
"properties": {
"max_cpus": {
"type": "integer",
"description": "Maximum number of CPUs that can be requested for any single job.",
"fa_icon": "fas fa-microchip",
"hidden": true,
"help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
},
"max_memory": {
"type": "string",
"description": "Maximum amount of memory that can be requested for any single job.",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"hidden": true,
"help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
}
}
},
"generic_options": {
"title": "Generic options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Less common options for the pipeline, typically set in a config file.",
"help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
"properties": {
"help": {
"type": "boolean",
"description": "Display help text.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"version": {
"type": "boolean",
"description": "Display the version of the pipeline.",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"email_on_fail": {
"type": "string",
"description": "Email address for completion summary, only when pipeline fails.",
"fa_icon": "fas fa-exclamation-triangle",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"fa_icon": "fas fa-cogs",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"show_hidden_params": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"enable_conda": {
"type": "boolean",
"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"hidden": true,
"fa_icon": "fas fa-bacon"
},
"monochrome_logs": {
"type": "boolean",
"description": "",
"hidden": false,
"fa_icon": "fas fa-bacon"
},
"singularity_cache_dir": {
"type": "string",
"description": "The path to store singularity containers locally to be reused later",
"hidden": false,
"fa_icon": "fas fa-bacon"
},
"hook_url": {
"type": "string",
"description": "Incoming hook URL for messaging service",
"fa_icon": "fas fa-people-group",
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
}
}
},
"saved_output_options": {
"title": "Pipeline output options",
"type": "object",
"fa_icon": "fas fa-file-import",
"description": "Decide on what processes output to keep.",
"help_text": "",
"properties": {
"fastq_suffix": {
"type": "string",
"description": ".",
"default": "fastq",
"fa_icon": "fas fa-question-circle",
"hidden": true
},
"publish_dir_mode": {
"type": "string",
"default": "copy",
"description": "Method used to save pipeline results to output directory.",
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
"fa_icon": "fas fa-copy",
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
},
"phylogeny_make_alignments_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'phylogeny_make_alignments' will be saved in the output directory.",
"help_text": "process output is a collection of raw alignments, where each file represents a single locus and contains unaligned sequence data for all recovered samples",
"fa_icon": "fas fa-copy",
"hidden": true
},
"assembly_postprocessing_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'assembly_postprocessing' will be saved in the output directory.",
"help_text": "process output for each sample is a single fasta file containing all assembled contigs, as well as a directory with all Trinity output files (inchworm, jellyfish, read normalization files). Each sample directory can be very large (>3G), so we do not recommend retaining these files.",
"fa_icon": "fas fa-copy",
"hidden": true
},
"trimmomatic_clean_pe_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'trimmomatic_clean_pe' will be saved in the output directory.",
"help_text": "process output for each sample are forward and reverse, paired and unpaired fq.gz files (4 total). These are the result of leading/trailing read trimming.",
"fa_icon": "fas fa-copy",
"hidden": true
},
"trimmomatic_clean_se_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'trimmomatic_clean_se' will be saved in the output directory.",
"help_text": "process output for each sample is a single unpaired fq.gz file. This is the result of leading/trailing read trimming.",
"fa_icon": "fas fa-copy",
"hidden": true
},
"parse_blat_results_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'parse_blat_results' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"quality_2_assembly_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'quality_2_assembly' will be saved in the output directory.",
"help_text": "process output for each sample is a csv file summarizing the target coverage (number of contigs, AHE, UCE, gene tallies)",
"fa_icon": "fas fa-copy",
"hidden": true
},
"samplesheet_check_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'samplesheet_check' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"bbmap_reformat_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'bbmap_reformat' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"prepare_adaptor_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'prepare_adaptor' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"convert_phyml_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'convert_phyml' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"preprocessing_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'preprocessing' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"bbmap_dedupe_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'bbmap_dedupe' will be saved in the output directory.",
"help_text": "process output for each sample are a fq.gz file of deduplicated reads, and another fq.gz file of duplicates",
"fa_icon": "fas fa-copy",
"hidden": true
},
"bbmap_filter_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'bbmap_filter' will be saved in the output directory.",
"help_text": "process output for each sample are forward and reverse reads that have been filtered against a set of phylogenetically informed targets",
"fa_icon": "fas fa-copy",
"hidden": true
},
"perl_cleanup_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'perl_cleanup' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"concatenate_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'concatenate' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"merge_trees_keep_output": {
"type": "boolean",
"default": true,
"description": "If enabled, the output of process 'merge_trees' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": false
},
"trimmomatic_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'trimmomatic' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"make_prg_keep_output": {
"type": "boolean",
"default": true,
"description": "If enabled, the output of process 'make_prg' will be saved in the output directory.",
"help_text": "process output for each sample is a single Pseudo-Reference-Genome fasta file holding the successfully assembled and annotated targets. These are worthile to retain.",
"fa_icon": "fas fa-copy",
"hidden": false
},
"gblocks_keep_output": {
"type": "boolean",
"default": true,
"description": "If enabled, the output of process 'gblocks' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": false
},
"testing_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'testing' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"trinity_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'trinity' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"iqtree_keep_output": {
"type": "boolean",
"default": true,
"description": "If enabled, the output of process 'iqtree' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": false
},
"aster_keep_output": {
"type": "boolean",
"default": true,
"description": "If enabled, the output of process 'aster' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": false
},
"macse_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'macse' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"mafft_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'mafft' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"raxml_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'raxml' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"blat_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'blat' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"pear_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'pear' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"sed_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'sed' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
},
"spades_keep_output": {
"type": "boolean",
"default": false,
"description": "If enabled, the output of process 'SPAdes' will be saved in the output directory.",
"help_text": "",
"fa_icon": "fas fa-copy",
"hidden": true
}
}
},
"phylogeny_make_alignments_options": {
"title": "phylogeny_make_alignments options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process phylogeny_make_alignments.",
"help_text": "",
"properties": {
"phylogeny_make_alignments_args": {
"type": "string",
"default": "--minsamp 4",
"description": "The arguments to be passed to process (phylogeny_make_alignments).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"phylogeny_make_alignments_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (phylogeny_make_alignments).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"phylogeny_make_alignments_memory": {
"type": "string",
"description": "The requested memory for the process (phylogeny_make_alignments).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "4.GB"
},
"phylogeny_make_alignments_walltime": {
"type": "string",
"description": "The requested walltime for the process (phylogeny_make_alignments).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "4.h"
}
}
},
"assembly_postprocessing_options": {
"title": "assembly_postprocessing options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process assembly_postprocessing.",
"help_text": "",
"properties": {
"assembly_processed_header": {
"type": "string",
"default": "contig",
"description": "Prefix for a contig of assembled reads",
"help_text": "Naming convention for assembled contigs. Suggested Usage: contig",
"fa_icon": "fa fa-cog",
"hidden": true
},
"assembly_postprocessing_args": {
"type": "string",
"description": "",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"assembly_postprocessing_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (assembly_postprocessing).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"assembly_postprocessing_memory": {
"type": "string",
"description": "The requested memory for the process (assembly_postprocessing).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "4.GB"
},
"assembly_postprocessing_walltime": {
"type": "string",
"description": "The requested walltime for the process (assembly_postprocessing).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "4.h"
}
}
},
"trimmomatic_clean_pe_options": {
"title": "trimmomatic_clean_pe options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process trimmomatic_clean_pe.",
"help_text": "",
"properties": {
"trimmomatic_clean_pe_args": {
"type": "string",
"default": "-phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36",
"description": "The arguments to be passed to process (trimmomatic_clean_pe).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"trimmomatic_clean_pe_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (trimmomatic_clean_pe).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"trimmomatic_clean_pe_memory": {
"type": "string",
"description": "The requested memory for the process (trimmomatic_clean_pe).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "4.GB"
},
"trimmomatic_clean_pe_walltime": {
"type": "string",
"description": "The requested walltime for the process (trimmomatic_clean_pe).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "4.h"
}
}
},
"trimmomatic_clean_se_options": {
"title": "trimmomatic_clean_se options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process trimmomatic_clean_se.",
"help_text": "",
"properties": {
"trimmomatic_clean_se_args": {
"type": "string",
"default": "-phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36",
"description": "The arguments to be passed to process (trimmomatic_clean_se).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"trimmomatic_clean_se_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (trimmomatic_clean_se).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"trimmomatic_clean_se_memory": {
"type": "string",
"description": "The requested memory for the process (trimmomatic_clean_se).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "4.GB"
},
"trimmomatic_clean_se_walltime": {
"type": "string",
"description": "The requested walltime for the process (trimmomatic_clean_se).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "4.h"
}
}
},
"parse_blat_results_options": {
"title": "parse_blat_results options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process parse_blat_results.",
"help_text": "",
"properties": {
"parse_blat_results_args": {
"type": "string",
"default": "--evalue 1e-10 --match 80",
"description": "The arguments to be passed to process (parse_blat_results).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"parse_blat_results_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (parse_blat_results).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"parse_blat_results_memory": {
"type": "string",
"description": "The requested memory for the process (parse_blat_results).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "8.GB"
},
"parse_blat_results_walltime": {
"type": "string",
"description": "The requested walltime for the process (parse_blat_results).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "12.h"
}
}
},
"quality_2_assembly_options": {
"title": "quality_2_assembly options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process quality_2_assembly.",
"help_text": "",
"properties": {
"quality_2_assembly_args": {
"type": "string",
"default": "",
"description": "The arguments to be passed to process (quality_2_assembly).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"quality_2_assembly_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (quality_2_assembly).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"quality_2_assembly_memory": {
"type": "string",
"description": "The requested memory for the process (quality_2_assembly).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "8.GB"
},
"quality_2_assembly_walltime": {
"type": "string",
"description": "The requested walltime for the process (quality_2_assembly).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "12.h"
}
}
},
"samplesheet_check_options": {
"title": "samplesheet_check options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process samplesheet_check.",
"help_text": "",
"properties": {
"samplesheet_check_args": {
"type": "string",
"default": "",
"description": "The arguments to be passed to process (samplesheet_check).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"samplesheet_check_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (samplesheet_check).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"samplesheet_check_memory": {
"type": "string",
"description": "The requested memory for the process (samplesheet_check).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "8.GB"
},
"samplesheet_check_walltime": {
"type": "string",
"description": "The requested walltime for the process (samplesheet_check).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "12.h"
}
}
},
"bbmap_reformat_options": {
"title": "bbmap_reformat options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process bbmap_reformat.",
"help_text": "",
"properties": {
"bbmap_reformat_args": {
"type": "string",
"default": "minconsecutivebases=100 dotdashxton=true fastawrap=32000",
"description": "The arguments to be passed to process (bbmap_reformat).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"bbmap_reformat_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (bbmap_reformat).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"bbmap_reformat_memory": {
"type": "string",
"description": "The requested memory for the process (bbmap_reformat).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "8.GB"
},
"bbmap_reformat_walltime": {
"type": "string",
"description": "The requested walltime for the process (bbmap_reformat).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "12.h"
}
}
},
"prepare_adaptor_options": {
"title": "prepare_adaptor options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process prepare_adaptor.",
"help_text": "",
"properties": {
"prepare_adaptor_args": {
"type": "string",
"default": "",
"description": "The arguments to be passed to process (prepare_adaptor).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"prepare_adaptor_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (prepare_adaptor).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"prepare_adaptor_memory": {
"type": "string",
"description": "The requested memory for the process (prepare_adaptor).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "2.GB"
},
"prepare_adaptor_walltime": {
"type": "string",
"description": "The requested walltime for the process (prepare_adaptor).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "1.h"
}
}
},
"convert_phyml_options": {
"title": "convert_phyml options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process convert_phyml.",
"help_text": "",
"properties": {
"convert_phyml_args": {
"type": "string",
"default": "",
"description": "The arguments to be passed to process (convert_phyml).",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"convert_phyml_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (convert_phyml).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"convert_phyml_memory": {
"type": "string",
"description": "The requested memory for the process (convert_phyml).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "8.GB"
},
"convert_phyml_walltime": {
"type": "string",
"description": "The requested walltime for the process (convert_phyml).",
"help_text": "",
"fa_icon": "far fa-clock",
"hidden": true,
"default": "12.h"
}
}
},
"preprocessing_options": {
"title": "preprocessing options",
"type": "object",
"fa_icon": "fa-solid fa-arrow-progress",
"description": "The configurations of the process preprocessing.",
"help_text": "",
"properties": {
"preprocessing_args": {
"type": "string",
"description": "",
"help_text": "",
"fa_icon": "fa fa-cog",
"hidden": true
},
"preprocessing_cpus": {
"type": "integer",
"description": "The number of requested CPUs for the process (preprocessing).",
"help_text": "",
"fa_icon": "fas fa-microchip",
"hidden": true,
"default": 1
},
"preprocessing_memory": {
"type": "string",
"description": "The requested memory for the process (preprocessing).",
"help_text": "",
"fa_icon": "fas fa-memory",
"hidden": true,
"default": "8.GB"