186 lines
7.6 KiB
JSON
186 lines
7.6 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
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"title": "epi2me-labs/wf-isoforms",
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"description": "Isoform detection and characterisation.",
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"url": "https://github.com/epi2me-labs/wf-isoforms",
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"type": "object",
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"definitions": {
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"basic_input_output_options": {
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"title": "Basic Input/Output Options",
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"properties": {
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"out_dir": {
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"type": "string",
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"default": "output",
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"description": "Directory for output of all user-facing files."
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},
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"fastq": {
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"type": "string",
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"format": "path",
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"description": "A fastq file or directory containing fastq input files or directories of input files.",
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"help_text": "If directories named \\\"barcode*\\\" are found under the `--fastq` directory the data is assumed to be multiplex and each barcode directory will be processed independently. If `.fastq(.gz)` files are found under the `--fastq` directory the sample is assumed to not be multiplexed. In this second case `--samples` should be a simple name rather than a CSV file."
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},
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"sample": {
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"type": "string",
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"description": "A sample name for non-multiplexed data. Permissible if passing a file or directory of .fastq(.gz)."
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},
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"sample_sheet": {
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"type": "string",
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"format": "file-path",
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"description": "CSV file with columns named `barcode`, `sample_name` and `type`. Permissible if passing a directory containing barcodeXX sub-directories."
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},
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"sanitize_fastq": {
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"type": "boolean",
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"description": "Use additional heuristics to identify barcodes from file paths.",
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"help_text": "Enabling this option will group together files into samples by the presence of strings of the form `barcodeXXX` present in filenames, rather than simply files grouped into directories (as output by MinKNOW and the Guppy basecaller)."
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},
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"plot_gffcmp_stats": {
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"type": "boolean",
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"description": "Create a pdf of plots from showing gffcompare results"
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},
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"gffcompare_opts": {
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"type": "string",
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"description": "Extra options for gffcompare -r",
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"default": " -R "
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},
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"ref_genome": {
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"type": "string",
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"format": "file-path",
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"description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]"
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},
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"ref_annotation": {
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"type": "string",
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"format": "file-path",
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"description": "A reference annotation of gff format"
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},
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"use_pychopper": {
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"type": "boolean",
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"description": "Use pychopper to preprcess reads",
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"default": true
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},
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"pychopper_opts": {
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"type": "string",
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"description": "Extra pychopper opts"
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},
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"threads": {
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"type": "integer",
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"default": 8
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},
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"minimap_index_opts": {
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"type": "string",
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"description": "minimap2 extra indexing options.",
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"default": "-k14"
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},
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"minimap2_opts": {
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"type": "string",
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"description": "minimap2 extra mapping options.",
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"default": "-uf"
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},
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"minimum_mapping_quality": {
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"type": "integer",
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"description": "filter aligned reads by MAPQ quality.",
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"default": 40
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},
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"poly_context": {
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"type": "integer",
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"description": "Region size at end of reads to apply poly(A) filter.",
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"default": 24
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},
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"max_poly_run": {
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"type": "integer",
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"description": "Max poly(A) region allowed with poly_context-sized end regions.",
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"default": 8
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},
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"bundle_min_reads": {
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"type": "integer",
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"description": "Minimum size of bam bundle for parallel processing."
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},
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"use_guide_annotation": {
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"type": "boolean",
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"description": "Use reference annotation in stringtie transcript assembly.",
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"default": "true"
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},
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"stringtie_opts": {
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"type": "string",
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"description": "Extra options for stringtie transcript assembly.",
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"default": " --conservative "
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},
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"disable_ping": {
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"type": "boolean"
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}
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},
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"required": [
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"fastq",
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"ref_genome"
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]
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},
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"meta_data": {
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"title": "Meta Data",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"report_name": {
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"type": "string",
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"default": "report",
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"description": "Output report filename suffix."
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}
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}
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},
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"generic_options": {
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"title": "Generic options",
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"type": "object",
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"fa_icon": "far fa-question-circle",
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"description": "Less common options for the pipeline, typically set in a config file.",
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"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`.",
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"properties": {
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"help": {
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"type": "boolean",
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"description": "Display help text.",
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"fa_icon": "fas fa-question-circle",
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"hidden": true
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/basic_input_output_options"
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},
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{
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"$ref": "#/definitions/meta_data"
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},
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{
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"$ref": "#/definitions/generic_options"
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}
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],
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"properties": {
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"aws_image_prefix": {
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"type": "string",
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"hidden": true
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},
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"aws_queue": {
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"type": "string",
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"hidden": true
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},
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"wfversion": {
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"type": "string",
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"default": "v0.3.3",
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"hidden": true
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},
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"monochrome_logs": {
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"type": "boolean"
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},
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"validate_params": {
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"type": "boolean",
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"default": true
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},
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"show_hidden_params": {
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"type": "boolean"
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}
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}
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}
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