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nextflow_schema.json
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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-nsvcalling/master/nextflow_schema.json",
"title": "nf-snvcalling pipeline parameters",
"description": "ODCF SNV calling pipeline",
"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",
"pattern": "^\\S+\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
},
"post_processes": {
"title": "Post process options",
"type": "object",
"description": "Options for post-processing after SNV calling",
"default": "",
"properties": {
"runSNVAnnotation": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Enable SNV Annotation"
},
"runSNVDeepAnnotation": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Enable SNV Deep Annotation with extra annotation files"
},
"runSNVVCFFilter": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Enable variant filtration"
},
"runArtifactFilter": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Enable Artifact filtration during annotation"
},
"runplots": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Produce plots for bias and error check"
},
"generateExtendedQcPlots": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Generate extended QC plots"
},
"runCompareGermline": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Enable comparison with germline variants (if available) during SNV call"
},
"runpurest": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Enable purest analysis"
},
"runcontigs": {
"type": "string",
"default": "NULL",
"fa_icon": "fas fa-post_processes",
"description": "Specify extra contig processing"
},
"annotation_tools": {
"type": "string",
"default": "NULL",
"fa_icon": "fas fa-post_processes",
"description": "Choose annovar or vep to perform annotation"
},
"report_json": {
"type": "boolean",
"default": "true",
"fa_icon": "fas fa-post_processes",
"description": "Reporting for VEP is not possible use only if using ANNOVAR"
},
"skip_multiqc": {
"type": "boolean",
"default": "false",
"fa_icon": "fas fa-post_processes",
"description": "Skip MultiQC"
}
}
},
"annotation_params": {
"title": "Annotation options",
"type": "object",
"description": "Options for Annotations",
"default": "",
"properties": {
"confidenceoptions": {
"type": "string",
"default": "-t 500",
"fa_icon": "fas fa-annotation",
"description": "List of options for confidence calculation"
},
"k_genome": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "1K genome VCF file, should be indexed. Column Name: 1K_GENOMES"
},
"dbsnp_snv": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "dbSNP SNV VCF file, should be indexed. Column Name: DBSNP"
},
"local_control_wgs": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "Local Exclusion list for WGS, VCF file, should be indexed. Column Name: LocalControlAF_WGS"
},
"local_control_wes": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "Local Exclusion list for WES, VCF file, should be indexed. Column Name: LocalControlAF_WeS"
},
"gnomad_genomes": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "Gnomad genomes VCF file, should be indexed. Column Name: GNOMAD_GENOMES"
},
"gnomad_exomes": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "Gnomad exomes VCF file, should be indexed. Column Name: GNOMAD_EXOMES"
}
}
},
"annovar_params": {
"title": "Annovar options",
"type": "object",
"description": "Options for Annovar",
"default": "",
"properties": {
"buildver": {
"type": "string",
"default": "hg19",
"fa_icon": "fas fa-annovar",
"description": "Annovar build version"
},
"dbtype": {
"type": "string",
"default": "wgEncodeGencodeCompV19",
"fa_icon": "fas fa-annovar",
"description": "Annovar dbtype"
},
"segdupcol": {
"type": "string",
"default": "SEGDUP",
"fa_icon": "fas fa-annovar",
"description": "Segmental duplication column name"
},
"cytobandcol": {
"type": "string",
"default": "CYTOBAND",
"fa_icon": "fas fa-annovar",
"description": "Cytobad column name"
},
"geneannocols": {
"type": "string",
"default": "ANNOVAR_FUNCTION,GENE,EXONIC_CLASSIFICATION,ANNOVAR_TRANSCRIPTS",
"fa_icon": "fas fa-annovar",
"description": "Column names seperated with ',' for annovar "
},
"annovar_path": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"fa_icon": "fas fa-annotation",
"description": "File path to annovar execution file: annovar/annovar_Feb2016/"
}
}
},
"vep_params": {
"title": "Annovar options",
"type": "object",
"description": "Options for Annovar",
"default": "",
"properties": {
"vep_cache_version": {
"type": "string",
"default": "110",
"fa_icon": "fas fa-vep",
"description": "VEP Cache version"
},
"vep_genome": {
"type": "string",
"default": "GRCh38",
"fa_icon": "fas fa-vep",
"description": "VEP genome"
},
"vep_cache": {
"format": "file-path",
"mimetype": "text/plain",
"default": "null",
"fa_icon": "fas fa-vep",
"description": "File path to the VEP cache"
},
"download_cache": {
"type": "boolean",
"default": "false",
"fa_icon": "fas fa-vep",
"description": "Turn it on to download cache file"
},
"outdir_cache": {
"type": "string",
"default": "null",
"fa_icon": "fas fa-annovar",
"description": "Cache file directory to save, if download_cache is true"
}
}
},
"snv_reliability_params": {
"title": "Indel Reability files",
"type": "object",
"description": "Options for indel reability",
"default": "",
"properties": {
"repeat_masker": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC repeat masker BED.GZ, should be indexed. Column Name:REPEAT_MASKER .NOTE: This file also used in Visualizations!"
},
"dac_blacklist": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC DAC blacklist BED.GZ, should be indexed. Column Name: DAC_BLACKLIST"
},
"duke_excluded": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC Duke Excluded BED.GZ, should be indexed. Column Name: DUKE_EXCLUDED"
},
"hiseq_depth": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC HiSeq Depth BED.GZ, should be indexed. Column Name: HISEQDEPTH"
},
"self_chain": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC self chain BED.GZ, should be indexed. Column Name: SELFCHAIN"
},
"mapability_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC wg Encode Mapability BED.GZ, should be indexed. Column Name: MAPABILITY"
},
"simple_tandemrepeats": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC simple tandem repeats BED.GZ, should be indexed. Column Name: SIMPLE_TANDEMREPEATS"
}
}
},
"deep_annotation_options": {
"title": "SNV Deep Annotation files",
"type": "object",
"description": "Options for runIndelDeepAnnotation",
"default": "",
"properties": {
"enchancer_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC Enhancers BED.GZ, should be indexed. Column Name: Enhancers"
},
"cpgislands_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC CpG islands BED.GZ, should be indexed. Column Name: CpGislands"
},
"tfbscons_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC TFBS sites BED.GZ, should be indexed. Column Name: TFBScons"
},
"encode_dnase_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC DNase cluster BED.GZ, should be indexed. Column Name: ENCODE_DNASE"
},
"mirnas_snornas_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "mirBase snoRNAs BED.GZ, should be indexed. Column Name: miRNAs_snoRNAs"
},
"mirna_sncrnas_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "mirBase sncRNAs BED.GZ, should be indexed. Column Name: miRNAs_sncRNAs"
},
"mirbase_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "mirBase miRNAs BED.GZ, should be indexed. Column Name: miRBase18"
},
"cosmic_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "COSMIC db coding SNVs BED.GZ, should be indexed. Column Name: COSMIC"
},
"mir_targets_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "mirBase miRNA Target sites BED.GZ, should be indexed. Column Name: miRNAtargets"
},
"cgi_mountains_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "Cgi Mountains BED.GZ, should be indexed. Column Name: CgiMountains"
},
"phastconselem_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC phast cons elements BED.GZ, should be indexed. Column Name: phastConsElem20bp"
},
"encode_tfbs_file": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.bed(\\.gz)?$",
"fa_icon": "fas fa-annotation",
"description": "UCSC TFBS clusters BED.GZ, should be indexed. Column Name: ENCODE_TFBS"
}
}
},
"filtration_params": {
"title": "Filtration options",
"type": "object",
"description": "Options for VCF Filtering",
"default": "",
"properties": {
"min_confidence_score": {
"type": "integer",
"default": "8",
"fa_icon": "fas fa-filter",
"description": "Minimum confidence score for filtration"
},
"allele_freq": {
"type": "integer",
"default": "0",
"fa_icon": "fas fa-filter",
"description": "ignore SNVs with MAF below that value (rainfall plot)"
},
"min_cov": {
"type": "integer",
"default": "0",
"fa_icon": "fas fa-filter",
"description": "minimal coverage for somatic SNVs (MAF plot)"
},
"crit_1kgenomes_maxmaf": {
"type": "number",
"default": "",
"fa_icon": "fas fa-annotation",
"description": "Max MAF for 1K_GENOME filtration. Only apply if annotation is done"
},
"crit_gnomad_exomes_maxmaf": {
"type": "number",
"default": "",
"fa_icon": "fas fa-annotation",
"description": "Max MAF for GNOMAD_GENOMES filtration. Only apply if annotation is done"
},
"crit_gnomad_genomes_maxmaf": {
"type": "number",
"default": "",
"fa_icon": "fas fa-annotation",
"description": "Max MAF for GNOMAD_EXOMES filtration. Only apply if annotation is done"
},
"crit_localcontrol_maxmaf": {
"type": "number",
"default": "",
"fa_icon": "fas fa-annotation",
"description": "Max MAF for Local Control filtration for the columns: LocalControlAF_WGS and LocalControlAF_WES. Only apply if annotation is done"
}
}
},
"visualization_params": {
"title": "Visualization options",
"type": "object",
"description": "Options for screenshots",
"default": "",
"properties": {
"plot_type": {
"type": "string",
"default": "Differences",
"fa_icon": "fas fa-filter",
"description": "Differences or Ratios "
}
}
},
"filter_bias_params": {
"title": "Filter Bias options",
"type": "object",
"description": "Options for filter_bias.py",
"default": "",
"properties": {
"biasPValThreshold": {
"type": "number",
"default": "0.01",
"fa_icon": "fas fa-filter",
"description": "probability threshold to accept bias. The p value gives the probability to observe the same or stronger bias by chance when assuming a binomial distribution with event probability of 0.5"
},
"biasRatioMinimum": {
"type": "number",
"default": "0.53",
"fa_icon": "fas fa-filter",
"description": "minimum fraction of reads in direction of bias / total variant reads we require to call a field biased"
},
"biasRatioThreshold": {
"type": "number",
"default": "0.63",
"fa_icon": "fas fa-filter",
"description": "threshold for fraction of reads in direction of bias / total variant reads above which it will be considered a strong bias"
},
"nReads": {
"type": "number",
"default": "20",
"fa_icon": "fas fa-filter",
"description": " number of reads in one field above which a bias is possible"
},
"nMuts": {
"type": "number",
"default": "4",
"fa_icon": "fas fa-filter",
"description": "number of muts above which a bias is possible"
},
"tha_score_threshold": {
"type": "number",
"default": "0.15",
"fa_icon": "fas fa-filter",
"description": "THA score threshold, Threshold for calling sample THA affected. Threshold refers to fraction of SNVs with BaseQ pVal below 0.05"
},
"median_filter_threshold": {
"type": "number",
"default": "20",
"fa_icon": "fas fa-filter",
"description": "SNVs with median of alternative base qualities below this threshold will be removed in the rerun filter step. Value of -1 means no filtering"
},
"rVcf": {
"type": "number",
"default": "0.1",
"fa_icon": "fas fa-filter",
"description": "max fraction of reads (reads/total reads) we tolerate in the direction opposite to the bias for it to be called an artefact"
},
"maxNumOppositeReadsSequencingWeakBias": {
"type": "number",
"default": "0",
"fa_icon": "fas fa-filter",
"description": "Maximum number of opposite reads for sequencing weak bias"
},
"maxNumOppositeReadsSequenceWeakBias": {
"type": "number",
"default": "0",
"fa_icon": "fas fa-filter",
"description": "Maximum number of opposite reads for sequence weak bias"
},
"maxNumOppositeReadsSequencingStrongBias": {
"type": "number",
"default": "1",
"fa_icon": "fas fa-filter",
"description": "Maximum number of reads for sequencing strong bias"
},
"maxNumOppositeReadsSequenceStrongBias": {
"type": "number",
"default": "1",
"fa_icon": "fas fa-filter",
"description": "Maximum number of reads for sequence strong bias"
}
}
},
"filter_pe_overlap_params": {
"title": "Filter_PE_Overlap options",
"type": "object",
"description": "Options for filter_PEoverlap.py",
"default": "",
"properties": {
"basequal": {
"type": "number",
"default": "13",
"fa_icon": "fas fa-annotation",
"description": "Base Quality used for SNV calling"
},
"mapqual": {
"type": "number",
"default": "30",
"fa_icon": "fas fa-annotation",
"description": "MAP Quality used for SNV calling"
},
"bottom_border": {
"type": "number",
"default": "0.01",
"fa_icon": "fas fa-annotation",
"description": "Bottom border for Canopy based clustering"
},
"qualityscore": {
"type": "string",
"default": "Phred",
"fa_icon": "fas fa-annotation",
"description": "Quality score type"
},
"mismatch_threshold": {
"type": "number",
"default": "-1",
"fa_icon": "fas fa-annotation",
"description": "Mismatch threshold for PE overlap filtration"
}
}
},
"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
"fa_icon": "fas fa-dna",
"description": "Reference genome related files and options required for the workflow.",
"properties": {
"genome": {
"type": "string",
"description": "Name of iGenomes reference.",
"fa_icon": "fas fa-book",
"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
},
"ref_type": {
"type": "string",
"description": "Name of reference.",
"fa_icon": "fas fa-book",
"help_text": "If using a reference genome configured in ODCF cluster, use this parameter to give the ID for the reference.hg 37 or hg19."
},
"fasta": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--ref_type` is not specified.",
"fa_icon": "far fa-file-code"
},
"igenomes_base": {
"type": "string",
"format": "directory-path",
"description": "Directory / URL base for iGenomes references.",
"default": "s3://ngi-igenomes/igenomes",
"fa_icon": "fas fa-cloud-download-alt",
"hidden": true
},
"igenomes_ignore": {
"type": "boolean",
"description": "Do not load the iGenomes reference config.",
"fa_icon": "fas fa-ban",
"hidden": true,
"help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
}
}
},
"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.",
"default": 16,
"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.",
"default": "128.GB",
"fa_icon": "fas fa-memory",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"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
},
"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
},
"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})$",
"help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.",
"hidden": true
},
"plaintext_email": {
"type": "boolean",
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
},
"multiqc_config": {
"type": "string",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${params.outdir}/pipeline_info",
"fa_icon": "fas fa-cogs",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"show_hidden_params": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"enable_conda": {
"type": "boolean",
"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"hidden": true,
"fa_icon": "fas fa-bacon"
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}