284 lines
9.8 KiB
JSON
284 lines
9.8 KiB
JSON
{
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"$schema": "http://json-schema.org/draft-07/schema",
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"$id": "https://raw.githubusercontent.com/epi2me-labs/wf-transcriptomes/master/nextflow_schema.json",
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"title": "epi2me-labs/wf-transcriptomes",
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"workflow_title": "Transcriptomes",
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"description": "Long-read transcript discovery, quantification, differential expression, QC and mod counting.",
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"demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/v2/wf-transcriptomes-demo.tar.gz",
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"aws_demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-transcriptomes/wf-transcriptomes-demo/transcriptomes.v2.aws.nextflow.config",
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"url": "https://github.com/epi2me-labs/wf-transcriptomes",
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"type": "object",
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"definitions": {
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"main_options": {
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"title": "Main Options",
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"type": "object",
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"description": "Parameters for read ingestion, and setting reference and transcriptome construction mode.",
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"properties": {
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"fastq": {
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"type": "string",
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"format": "path",
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"title": "FASTQ",
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"description": "FASTQ reads to analyse.",
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"help_text": "You can provide a single FASTQ, a folder of FASTQs, or a multiplexed folder containing one sub-folder per sample or barcode."
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},
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"bam": {
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"type": "string",
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"format": "path",
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"description": "BAM or uBAM reads to analyse.",
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"help_text": "You can provide a single BAM or uBAM, a folder of BAMs, or a multiplexed folder containing one sub-folder per sample or barcode."
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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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"title": "Reference genome",
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"description": "Reference genome FASTA.",
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"help_text": "Required in both discover and fixed_annotation modes."
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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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"title": "Reference annotation",
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"description": "Reference transcript annotation in GTF or GFF format.",
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"help_text": "Required in both discover and fixed_annotation modes."
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},
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"transcriptome_mode": {
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"type": "string",
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"default": "discover",
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"enum": [
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"discover",
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"fixed_annotation"
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],
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"description": "How bambu should prepare the transcriptome model.",
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"help_text": "Use discover for reference-guided transcript discovery and quantification, or fixed_annotation for quantification only against the supplied annotation."
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},
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"direct_rna": {
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"type": "boolean",
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"default": false,
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"description": "Set this for direct RNA sequencing libraries."
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}
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},
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"required": [
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"ref_genome",
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"ref_annotation",
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"transcriptome_mode"
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],
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"allOf": [
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{
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"oneOf": [
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{
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"required": [
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"fastq"
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]
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},
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{
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"required": [
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"bam"
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]
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}
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]
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}
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]
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},
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"filter_options": {
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"title": "Read Filtering Options",
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"type": "object",
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"description": "Options for filtering input reads.",
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"properties": {
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"analyse_unclassified": {
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"type": "boolean",
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"default": false,
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"description": "Include unclassified reads from multiplexed input directories."
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},
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"analyse_fail": {
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"type": "boolean",
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"default": false,
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"description": "Include fail reads from bam_fail and fastq_fail folders found in sample folders on the input path."
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}
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}
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},
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"sample_options": {
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"title": "Sample Options",
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"type": "object",
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"description": "Parameters that control sample naming and experimental design.",
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"properties": {
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"sample_sheet": {
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"type": "string",
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"format": "file-path",
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"title": "Sample sheet",
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"description": "CSV file describing barcodes, aliases, and optional experimental design columns.",
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"help_text": "For multiplexed runs, the sample sheet should contain both barcode and alias. Additionally, for differential analysis, it must also contain the condition column, and any extra columns named in `--covariates`."
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},
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"sample": {
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"type": "string",
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"description": "Single sample name for singleplexed input or to restrict multiplexed analysis to one sample."
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}
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}
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},
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"de_analysis_options": {
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"title": "Differential Expression Analysis Options",
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"type": "object",
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"description": "Parameters controlling DGE and DTU analyses.",
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"properties": {
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"de_analysis": {
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"type": "boolean",
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"default": false,
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"description": "Run differential gene expression and differential transcript usage analyses."
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},
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"condition_column": {
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"type": "string",
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"default": "condition",
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"description": "Main comparison column in the sample sheet."
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},
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"covariates": {
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"type": "string",
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"description": "Comma-separated extra sample-sheet columns to adjust for, for example batch.",
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"help_text": "Each listed name must exist as a column in the sample sheet."
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},
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"reference_level": {
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"type": "string",
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"description": "Baseline group for the main comparison column.",
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"help_text": "If omitted, the workflow will use control when that level exists."
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}
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},
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"dependencies": {
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"de_analysis": [
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"sample_sheet"
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]
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}
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},
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"output_options": {
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"title": "Output Options",
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"type": "object",
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"description": "Parameters controlling workflow outputs.",
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"properties": {
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"out_dir": {
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"type": "string",
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"format": "directory-path",
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"default": "output",
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"description": "Directory for user-facing workflow outputs."
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},
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"igv": {
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"type": "boolean",
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"default": false,
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"description": "Generate an IGV configuration file for the aligned BAM outputs."
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}
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}
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},
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"advanced_options": {
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"title": "Advanced Options",
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"type": "object",
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"description": "Performance tuning and tool-specific advanced parameters.",
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"properties": {
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"mod_codes": {
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"type": "string",
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"description": "Comma-separated modified base codes to pass to modkit pileup.",
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"help_text": "Provide values accepted by `modkit pileup --modified-bases`, for example `A:a,C:m`. If omitted, the workflow infers `primary_base:mod_code` pairs from the BAM with `modkit modbam check-tags`."
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},
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"force_alignment" : {
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"type": "boolean",
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"default": false,
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"description": "Force re-alignment of input BAM files.",
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"help_text": "Read alignment is skipped if the existing sequence names in the aligned BAM match the provided reference. Enable this if the existing alignments used incorrect minimap2 presets (e.g. missing --splice or direct RNA settings)."
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},
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"ndr": {
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"type": "number",
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"description": "Optional bambu novel discovery rate override.",
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"help_text": "Lower values are more conservative (higher precision), while higher values are more permissive (higher novel-discovery sensitivity). See the [`bambu` repository](https://github.com/GoekeLab/bambu) for method details."
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},
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"sqanti_skip_orf": {
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"type": "boolean",
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"default": true,
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"description": "Skip ORF prediction during SQANTI3 QC."
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}
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}
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},
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"misc": {
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"title": "Miscellaneous Options",
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"type": "object",
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"description": "Everything else.",
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"default": "",
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"properties": {
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"disable_ping": {
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"type": "boolean",
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"default": false,
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"description": "Enable to prevent sending a workflow ping.",
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"overrides": {
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"epi2mecloud": {
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"hidden": true
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}
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}
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},
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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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"default": false,
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"hidden": true
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},
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"version": {
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"type": "boolean",
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"description": "Display version and exit.",
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"fa_icon": "fas fa-question-circle",
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"default": false,
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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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"$ref": "#/definitions/main_options"
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},
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{
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"$ref": "#/definitions/filter_options"
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},
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{
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"$ref": "#/definitions/sample_options"
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},
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{
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"$ref": "#/definitions/de_analysis_options"
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},
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{
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"$ref": "#/definitions/output_options"
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},
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{
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"$ref": "#/definitions/advanced_options"
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},
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{
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"$ref": "#/definitions/misc"
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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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"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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"resources": {
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"recommended": {
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"cpus": 32,
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"memory": "96GB"
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},
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"minimum": {
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"cpus": 12,
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"memory": "64GB"
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},
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"run_time": "Varies with read depth and sample count; a small (1-5 million reads) single-sample run may finish in under 60 minutes with the recommended resources. Compute requirements are influenced most by total read count, reference complexity, number of samples, and whether optional steps such as DE/DTU, and modified-base summarisation are enabled.",
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"arm_support": false
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}
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}
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