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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-core/rnasplice/master/nextflow_schema.json",
"title": "nf-core/rnasplice pipeline parameters",
"description": "Alternative splicing analysis using RNA-seq.",
"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", "source", "outdir", "contrasts"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/rnasplice/usage#samplesheet-input).",
"fa_icon": "fas fa-file-csv"
},
"contrasts": {
"type": "string",
"description": "Path to comma-separated file containing information about the contrasts in the experiment."
},
"source": {
"type": "string",
"default": "fastq",
"enum": ["fastq", "genome_bam", "transcriptome_bam", "salmon_results"],
"description": "Source of input files."
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open"
},
"email": {
"type": "string",
"description": "Email address for completion summary.",
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"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"
},
"save_merged_fastq": {
"type": "boolean",
"description": "Save FastQ files after merging re-sequenced libraries in the results directory.",
"fa_icon": "fas fa-save"
}
}
},
"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."
},
"fasta": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"fa_icon": "far fa-file-code"
},
"gtf": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.gtf(\\.gz)?$",
"description": "Path to GTF annotation file.",
"fa_icon": "fas fa-code-branch",
"help_text": "This parameter is *mandatory* if `--genome` is not specified."
},
"gff": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.gff(\\.gz)?$",
"fa_icon": "fas fa-code-branch",
"description": "Path to GFF3 annotation file.",
"help_text": "This parameter must be specified if `--genome` or `--gtf` are not specified."
},
"transcript_fasta": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "far fa-file-code",
"description": "Path to FASTA transcriptome file."
},
"star_index": {
"type": "string",
"format": "path",
"fa_icon": "fas fa-bezier-curve",
"description": "Path to directory or tar.gz archive for pre-built STAR index."
},
"salmon_index": {
"type": "string",
"format": "path",
"fa_icon": "fas fa-bezier-curve",
"description": "Path to directory or tar.gz archive for pre-built Salmon index."
},
"gencode": {
"type": "boolean",
"description": "Specify if your transcript FASTA file is in GENCODE format.",
"help_text": "If your file is in GENCODE format and you would like to run Salmon i.e. `--pseudo_aligner salmon`, you will need to provide this parameter in order to build the Salmon index appropriately.",
"fa_icon": "fas fa-code-branch"
},
"gtf_extra_attributes": {
"type": "string",
"default": "gene_name",
"fa_icon": "fas fa-layer-group",
"description": "By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon."
},
"gtf_group_features": {
"type": "string",
"default": "gene_id",
"fa_icon": "fas fa-layer-group",
"description": "Define the attribute type used to group features in the GTF file when running Salmon."
},
"save_reference": {
"type": "boolean",
"fa_icon": "fas fa-save",
"description": "If generated by the pipeline save the STAR index in the results directory.",
"help_text": "If an alignment index is generated by the pipeline use this parameter to save it to your results folder. These can then be used for future pipeline runs, reducing processing times."
},
"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$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
"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 version and exit.",
"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
},
"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
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_methods_description": {
"type": "string",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"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
},
"validationShowHiddenParams": {
"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."
},
"validationFailUnrecognisedParams": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters fails when an unrecognised parameter is found.",
"hidden": true,
"help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
},
"validationLenientMode": {
"type": "boolean",
"fa_icon": "far fa-check-circle",
"description": "Validation of parameters in lenient more.",
"hidden": true,
"help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
}
}
},
"read_trimming_options": {
"title": "Read trimming options",
"type": "object",
"description": "Options to adjust read trimming criteria.",
"default": "",
"fa_icon": "fas fa-cut",
"properties": {
"clip_r1": {
"type": "integer",
"fa_icon": "fas fa-cut",
"description": "Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads)."
},
"clip_r2": {
"type": "integer",
"fa_icon": "fas fa-cut",
"description": "Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only)."
},
"three_prime_clip_r1": {
"type": "integer",
"fa_icon": "fas fa-cut",
"description": "Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed."
},
"three_prime_clip_r2": {
"type": "integer",
"fa_icon": "fas fa-cut",
"description": "Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed."
},
"trim_nextseq": {
"type": "integer",
"help_text": "This enables the option Cutadapt `--nextseq-trim=3'CUTOFF` option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.",
"fa_icon": "fas fa-cut",
"description": "Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails."
},
"save_trimmed": {
"type": "boolean",
"description": "Save the trimmed FastQ files in the results directory.",
"fa_icon": "fas fa-save"
},
"skip_trimming": {
"type": "boolean",
"description": "Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.",
"fa_icon": "fas fa-fast-forward"
},
"skip_trimgalore_fastqc": {
"type": "boolean",
"description": "Skip TrimGalore! FastQC.",
"fa_icon": "fas fa-fast-forward"
},
"min_trimmed_reads": {
"type": "integer",
"default": 10000,
"fa_icon": "fas fa-hand-paper",
"description": "Minimum number of trimmed reads below which samples are flagged in multiqc output."
}
}
},
"qc_options": {
"title": "QC options",
"type": "object",
"description": "Defube QC options required for the workflow.",
"default": "",
"fa_icon": "fas fa-chart-pie",
"properties": {
"skip_fastqc": {
"type": "boolean",
"description": "Skip FastQC.",
"fa_icon": "fas fa-fast-forward"
},
"skip_bigwig": {
"type": "boolean",
"default": true,
"description": "Skip bigWig file creation.",
"fa_icon": "fas fa-fast-forward"
}
}
},
"alignment_options": {
"title": "Alignment options",
"type": "object",
"description": "Options to adjust parameters and filtering criteria for read alignments.",
"default": "",
"fa_icon": "fas fa-map-signs",
"properties": {
"aligner": {
"type": "string",
"default": "star",
"description": "Specifies the alignment algorithm to use - available options are 'star_salmon', or 'star'.",
"fa_icon": "fas fa-map-signs"
},
"pseudo_aligner": {
"type": "string",
"default": "salmon",
"description": "Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner'.",
"enum": ["salmon"],
"fa_icon": "fas fa-hamburger"
},
"bam_csi_index": {
"type": "boolean",
"description": "Create a CSI index for BAM files instead of the traditional BAI index. This will be required for genomes with larger chromosome sizes.",
"fa_icon": "fas fa-sort-alpha-down"
},
"star_ignore_sjdbgtf": {
"type": "boolean",
"description": "When using pre-built STAR indices do not re-extract and use splice junctions from the GTF file.",
"fa_icon": "fas fa-ban"
},
"salmon_quant_libtype": {
"type": "string",
"fa_icon": "fas fa-fast-forward",
"description": " Override Salmon library type inferred based on strandedness defined in meta object.",
"help_text": "See [Salmon docs](https://salmon.readthedocs.io/en/latest/library_type.html)."
},
"seq_center": {
"type": "string",
"description": "Sequencing center information to be added to read group of BAM files.",
"fa_icon": "fas fa-synagogue"
},
"skip_alignment": {
"type": "boolean",
"description": "Skip all of the alignment-based processes within the pipeline."
},
"save_unaligned": {
"type": "boolean",
"description": "Where possible, save unaligned reads from either STAR or Salmon to the results directory."
},
"save_align_intermeds": {
"type": "boolean",
"description": "Save the intermediate BAM files from the alignment step.",
"help_text": "By default, intermediate BAM files will not be saved. The final BAM files created after the appropriate filtering step are always saved to limit storage usage. Set this parameter to also save other intermediate BAM files."
}
}
},
"rmats_options": {
"type": "object",
"title": "rMATS options",
"default": "",
"properties": {
"rmats": {
"type": "boolean",
"description": "Run rMATS workflow."
},
"rmats_splice_diff_cutoff": {
"type": "number",
"default": 0.0001,
"description": "The cutoff used in the null hypothesis test for differential splicing."
},
"rmats_paired_stats": {
"type": "boolean",
"default": true,
"description": "Use paired statistical model."
},
"rmats_read_len": {
"type": "integer",
"default": 40,
"description": "The length of each read."
},
"rmats_novel_splice_site": {
"type": "boolean",
"description": "Detect splicing events that involve an unannotated splice site."
},
"rmats_min_intron_len": {
"type": "integer",
"default": 50,
"description": "Minimum Intron Length."
},
"rmats_max_exon_len": {
"type": "integer",
"default": 500,
"description": "Maximum exon length."
}
},
"fa_icon": "far fa-chart-bar"
},
"dexseq_deu_options": {
"title": "DEXSeq DEU options",
"type": "object",
"description": "",
"default": "",
"properties": {
"dexseq_exon": {
"type": "boolean",
"description": "Run DEXSeq differential exon usage workflow."
},
"save_dexseq_annotation": {
"type": "boolean",
"description": "Save pre-processed GFF annotation file."
},
"gff_dexseq": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "^\\S+\\.gff(\\.gz)?$",
"fa_icon": "fas fa-code-branch",
"description": "Path to GFF3 annotation file."
},
"alignment_quality": {
"type": "integer",
"default": 10,
"description": "Minimum alignment quality required for reads to be counted."
},
"aggregation": {
"type": "boolean",
"default": true,
"description": "Combine overlapping genes into a single aggregate gene."
},
"save_dexseq_plot": {
"type": "boolean",
"default": true,
"description": "Save plots of the per gene DEXSeq results."
},
"n_dexseq_plot": {
"type": "integer",
"default": 10,
"description": "Plot the N most significant genes from the DEXSeq results."
}
},
"fa_icon": "far fa-chart-bar"
},
"edger_deu_options": {
"title": "edgeR DEU options",
"type": "object",
"description": "",
"default": "",
"properties": {
"edger_exon": {
"type": "boolean",
"description": "Run edgeR workflow."
},
"save_edger_plot": {
"type": "boolean",
"default": true,
"description": "Save plots of the per gene edgeR results."
},
"n_edger_plot": {
"type": "integer",
"default": 10,
"description": "Plot the N most significant genes from the edgeR results."
}
},
"fa_icon": "far fa-chart-bar"
},
"dexseq_dtu_options": {
"title": "DEXSeq DTU options",
"type": "object",
"description": "",
"default": "",
"properties": {
"dexseq_dtu": {
"type": "boolean",
"description": "Run DEXSeq differential transcript usage workflow."
},
"dtu_txi": {
"type": "string",
"default": "dtuScaledTPM",
"enum": ["dtuScaledTPM", "scaledTPM"],
"description": "Generate estimated counts using dtuScaledTPM or scaledTPM abundance estimates."
},
"min_samps_gene_expr": {
"type": "integer",
"default": 6,
"description": "Minimal number of samples where genes should be expressed."
},
"min_samps_feature_expr": {
"type": "integer",
"default": 0,
"description": "Minimal number of samples where features should be expressed."
},
"min_samps_feature_prop": {
"type": "integer",
"default": 0,
"description": "Minimal proportion of samples where features should be expressed."
},
"min_gene_expr": {
"type": "integer",
"default": 10,
"description": "Minimal gene expression."
},
"min_feature_expr": {
"type": "integer",
"default": 10,
"description": "Minimal feature expression."
},
"min_feature_prop": {
"type": "number",
"default": 0.1,
"description": "Minimal proportion for feature expression. This value should be between 0 and 1."
}
},
"fa_icon": "far fa-chart-bar"
},
"miso": {
"title": "Miso",
"type": "object",
"description": "",
"default": "",
"properties": {
"sashimi_plot": {
"type": "boolean",
"description": "Create sashimi plots using MISO."
},
"miso_genes": {
"type": "string",
"default": "ENSG00000004961, ENSG00000005302",
"description": "List containing identifiers of genes to plot."
},
"miso_genes_file": {
"type": "string",
"default": "None",
"description": "New-line separate file containing identifiers of genes to plot."
},
"miso_read_len": {
"type": "integer",
"default": 75,
"description": "Read length used to calculate coverage."
},
"fig_height": {
"type": "integer",
"default": 7,
"description": "Sashimi figure height (inches)."
},
"fig_width": {
"type": "integer",
"default": 7,
"description": "Sashimi figure width (inches)."
}
}
},
"suppa_options": {
"title": "SUPPA options",
"type": "object",
"description": "",
"default": "",
"properties": {
"suppa": {
"type": "boolean",
"default": true,
"description": "Run SUPPA workflow."
},
"suppa_per_local_event": {
"type": "boolean",
"default": true,
"description": "Quantify event inclusion levels (PSIs) from multiple samples."
},
"suppa_per_isoform": {
"type": "boolean",
"default": true,
"description": "Quantify isoform inclusion levels (PSIs) from multiple samples."
},
"suppa_tpm": {
"type": "string",
"format": "path",
"fa_icon": "fas fa-bezier-curve",
"help_text": "An example can be found at \"${projectDir}/assets/tpm.txt\"",
"description": "Expression file containing the abundances of all transcripts (ideally in TPM units)."
},
"generateevents_pool_genes": {
"type": "boolean",
"default": true,
"description": "Redefine genes by clustering together transcripts by genomic stranded overlap and sharing at least one exon."
},
"generateevents_event_type": {
"type": "string",
"default": "SE SS MX RI FL",
"description": "Space separated list of events to generate."
},
"generateevents_boundary": {
"type": "string",
"default": "S",
"description": "Boundary type (only used for local AS events).",
"enum": ["S", "V"]
},
"generateevents_threshold": {
"type": "integer",
"default": 10,
"description": "Variability treshold."
},
"generateevents_exon_length": {
"type": "integer",
"default": 100,
"description": "Defines the number of nucleotides to display in the output GTF."
},
"psiperevent_total_filter": {
"type": "integer",
"default": 0,
"description": "Minimum total expression of the transcripts involved in the event."
},
"diffsplice_local_event": {
"type": "boolean",
"default": true,
"description": "Calculate differential splicing for AS events across multiple conditions with replicates."
},
"diffsplice_isoform": {
"type": "boolean",
"default": true,
"description": "Calculate differential splicing for differential transcript usage across multiple conditions with replicates"
},
"diffsplice_method": {
"type": "string",
"default": "empirical",
"enum": ["empirical", "classical"],
"description": "The method to use to calculate the significance."
},
"diffsplice_area": {
"type": "integer",
"default": 1000,
"description": "Integer indicating the number of points in the local area of the delta PSI - average TPM distribution."
},
"diffsplice_lower_bound": {
"type": "integer",
"default": 0,
"description": "Lower-bound for the absolute delta PSI value to test for significance."
},
"diffsplice_gene_correction": {
"type": "boolean",
"default": true,
"description": "Correct the p-values by gene."
},
"diffsplice_paired": {
"type": "boolean",
"default": true,
"description": "Indicates if replicates across conditions are paired."
},
"diffsplice_alpha": {
"type": "number",
"default": 0.05,
"description": "Family-wise error rate to use for the multiple test correction."
},
"diffsplice_median": {
"type": "boolean",
"description": "Use the median to calculate the Delta PSI, instead of the mean."
},
"diffsplice_tpm_threshold": {
"type": "integer",
"default": 0,
"description": "Minimum expression (calculated as average TPM value within-replicates and between-conditions) to be included in the analysis."
},
"diffsplice_nan_threshold": {
"type": "integer",
"default": 0,
"description": "Proportion of samples with nan values allowed per condition to calculate a DeltaPSI ."
},
"clusterevents_local_event": {
"type": "boolean",
"default": true,
"description": "Cluster events according to PSI values across conditions"
},
"clusterevents_isoform": {
"type": "boolean",
"default": true,
"description": "Cluster transcripts according to PSI values across conditions"
},
"clusterevents_sigthreshold": {
"type": "number",
"description": "P-value threshold to consider an event significant from the dpsi file."
},
"clusterevents_dpsithreshold": {
"type": "number",
"default": 0.05,
"description": "Lower-bound for the absolute delta PSI value to cluster."
},
"clusterevents_eps": {
"type": "number",
"default": 0.05,
"description": "Maximum distance (between 0 and 1) to consider two events as members of the same cluster."
},
"clusterevents_metric": {
"type": "string",
"default": "euclidean",
"enum": ["euclidean", "manhattan", "cosine"],
"description": "Distance metric."
},
"clusterevents_separation": {
"type": "integer",
"description": "Maximum distance in PSI space of an event to a cluster."
},
"clusterevents_min_pts": {
"type": "integer",
"default": 20,
"description": "Minimum number of events required per cluster."
},
"clusterevents_method": {
"type": "string",
"default": "DBSCAN",
"enum": ["OPTICS", "DBSCAN"],
"description": "Clustering method to use (DBSCAN, OPTICS)."
}
},
"fa_icon": "far fa-chart-bar"
}
},
"allOf": [
{
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
},
{
"$ref": "#/definitions/read_trimming_options"
},
{
"$ref": "#/definitions/qc_options"
},
{
"$ref": "#/definitions/alignment_options"
},
{
"$ref": "#/definitions/rmats_options"
},
{
"$ref": "#/definitions/dexseq_deu_options"
},
{
"$ref": "#/definitions/edger_deu_options"
},
{
"$ref": "#/definitions/dexseq_dtu_options"
},
{
"$ref": "#/definitions/miso"
},
{
"$ref": "#/definitions/suppa_options"
}
]
}