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schema.json
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schema.json
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{
"pipeline": "long-read-ampliseq",
"params": {
"Basecalling": {
"basecall": {
"default": "true",
"help_text": "Enables basecalling to convert raw signal data to nucleotide sequences."
},
"basecall_model": {
"default": "[email protected]",
"help_text": "Specifies the model for basecalling, which matches specific flow cell and chemistry."
},
"trim_adapters": {
"default": "all",
"help_text": "This is the the same as the default behavior. Any detected adapters or primers will be trimmed"
},
"barcode_kit_name": {
"default": ["SQK-NBD114-24"],
"help_text": "Specifies the barcode kit used for multiplexing samples."
},
"read_format": {
"default": "fastq",
"help_text": "Sets the output format for basecalled reads to FASTQ."
},
"dorado_local_path": {
"default": "",
"help_text": "Path to the local Dorado basecaller, if used."
}
},
"Output File Management": {
"keep_sorted_bam": {
"default": "true",
"help_text": "Retain sorted BAM files."
},
"keep_bam_files": {
"default": "false",
"help_text": "Save intermediate BAM files."
},
"save_fastqs": {
"default": "true",
"help_text": "Save basecalled reads in FASTQ format."
},
"save_trimmed": {
"default": "true",
"help_text": "Save reads with adapters trimmed."
},
"save_too_short": {
"default": "true",
"help_text": "Save reads that are too short."
},
"save_too_long": {
"default": "true",
"help_text": "Save reads that are too long."
}
},
"Quality Control": {
"qc_reads": {
"default": "true",
"help_text": "Perform quality control on reads."
},
"min_qscore": {
"default": 9,
"help_text": "Minimum quality score for reads."
},
"cutadapt_args": {
"default": "-e 0.15 --no-indels --overlap 18",
"help_text": "Parameters for Cutadapt to trim adapters with specific error tolerance and overlap requirements."
},
"lower_read_length_cutoff": {
"default": 450,
"help_text": "Minimum read length after trimming."
},
"upper_read_length_cutoff": {
"default": 800,
"help_text": "Maximum read length after trimming."
},
"coverage_reporting_thresholds": {
"default": "1,2,8,10,25,30,40,50,100",
"help_text": "Coverage (per-amplicon locus reads depth) thresholds for reporting."
},
"coverage_filtering_threshold": {
"default": "25",
"help_text": "Minimum coverage for filtering."
},
"multiqc_config": {
"default": "",
"help_text": "Path to MultiQC configuration file. Leave blank to use default"
}
},
"Reference Files": {
"reference": {
"default": "",
"help_text": "Path to the reference genome file. (mandatory)"
},
"raw_read_dir": {
"default": "",
"help_text": "Directory containing raw read files. (mandatory)"
},
"primers": {
"default": "",
"help_text": "Path to the primer sequences file. (mandatory)"
},
"target_regions_bed": {
"default": "",
"help_text": "Path to the BED file with target regions. (mandatory)"
},
"additional_metadata": {
"default": "",
"help_text": "Path to the metadata file linking samples to barcodes. (mandatory)"
}
},
"Variant Calling": {
"clair3_model": {
"default": "",
"help_text": "Path to the Clair3 model for variant calling. (mandatory)"
},
"clair3_min_coverage": {
"default": "8",
"help_text": "Minimum coverage for variant calling."
},
"remove_recombination": {
"default": "false",
"help_text": "Do not remove recombination events."
},
"raxml_base_model": {
"default": "GTR+G4",
"help_text": "Base model used by RAxML-NG for phylogenetic analysis; ascertainment bias correction may be added if using SNP-restricted alignment."
},
"raxml_threads": {
"default": 2,
"help_text": "Number of threads for RAxML."
},
"masking_quality": {
"default": 15,
"help_text": "Quality score minimum for masking. Scores below this will be replaced with a N."
}
},
"LSF Options": {
"queue_size": {
"default": 50,
"help_text": "Maximum number of jobs in the queue."
},
"submit_rate_limit": {
"default": "50/2min",
"help_text": "Rate limit for job submissions."
},
"monochrome_logs": {
"default": "false",
"help_text": "Logs will not be in monochrome."
}
}
}
}