Updated schema (1972e6d3) · Commits · Chaos / Cutandrun

nextflow_schema.json

+267 −229

Original line number	Diff line number	Diff line
		@@ -5,6 +5,121 @@
		"description": "Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes sequencing QC, spike-in normalisation, IgG control normalisation, peak calling and downstream peak analysis.",
		"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"
		],
		"properties": {
		"input": {
		"type": "string",
		"format": "file-path",
		"mimetype": "text/csv",
		"pattern": "^\\S+\\.csv$",
		"schema": "assets/schema_input.json",
		"description": "Path to comma-separated file containing information about the samples in the experiment.",
		"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re//usage#samplesheet-input).",
		"fa_icon": "fas fa-file-csv"
		},
		"outdir": {
		"type": "string",
		"description": "Path to the output directory where the results will be saved.",
		"default": "./results",
		"fa_icon": "fas fa-folder-open"
		},
		"email": {
		"type": "string",
		"description": "Email address for completion summary.",
		"fa_icon": "fas fa-envelope",
		"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
		"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
		},
		"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_reference": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus",
		"description": "Save reference data to output directory"
		},
		"save_merged_fastq": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus",
		"description": "Save any technical replicates that were merged to output directory"
		},
		"save_trimmed": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus",
		"description": "Save trimmed fastqs to output directory"
		},
		"save_spikein_aligned": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus",
		"description": "Save bam files aligned to the spike-in genome to output directory"
		},
		"save_unaligned": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus",
		"description": "Save unaligned sequences to output directory"
		},
		"save_align_intermed": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus",
		"description": "Save alignment intermediates to output directory (WARNING: can be very large)"
		},
		"aligner": {
		"type": "string",
		"default": "bowtie2",
		"hidden": true,
		"fa_icon": "fas fa-align-justify",
		"description": "Select aligner"
		}
		}
		},
		"trimming_options": {
		"title": "Trimming Options",
		"type": "object",
		"description": "",
		"default": "",
		"properties": {
		"clip_r1": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify",
		"description": "Trim galore param"
		},
		"clip_r2": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify",
		"description": "Trim galore param"
		},
		"three_prime_clip_r1": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify",
		"description": "Trim galore param"
		},
		"three_prime_clip_r2": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify",
		"description": "Trim galore param"
		},
		"trim_nextseq": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify",
		"description": "Trim galore param"
		}
		},
		"fa_icon": "fas fa-cut"
		},
		"reference_data_options": {
		"title": "Reference data options",
		"type": "object",
		@@ -19,15 +134,18 @@
		},
		"bowtie2": {
		"type": "string",
		"fa_icon": "fas fa-book"
		"fa_icon": "fas fa-book",
		"description": "Path to bowtie2 index"
		},
		"gtf": {
		"type": "string",
		"fa_icon": "fas fa-book"
		"fa_icon": "fas fa-book",
		"description": "Path to GTF annotation file"
		},
		"blacklist": {
		"type": "string",
		"fa_icon": "fas fa-book"
		"fa_icon": "fas fa-book",
		"description": "Path to genome blacklist"
		},
		"spikein_genome": {
		"type": "string",
		@@ -37,11 +155,13 @@
		},
		"spikein_bowtie2": {
		"type": "string",
		"fa_icon": "fas fa-book"
		"fa_icon": "fas fa-book",
		"description": "Path to spike-in bowtie2 index"
		},
		"spikein_fasta": {
		"type": "string",
		"fa_icon": "fas fa-book"
		"fa_icon": "fas fa-book",
		"description": "Path to spike-in fasta"
		},
		"fasta": {
		"type": "string",
		@@ -69,6 +189,140 @@
		}
		}
		},
		"pipeline_options": {
		"title": "Pipeline Options",
		"type": "object",
		"description": "",
		"default": "",
		"properties": {
		"minimum_alignment_q_score": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-sort-numeric-down",
		"description": "Filter reads below a q-score threshold"
		},
		"dedup_target_reads": {
		"type": "boolean",
		"fa_icon": "fas fa-clone",
		"description": "Deduplicate non-control reads"
		},
		"normalisation_c": {
		"type": "integer",
		"default": 10000,
		"hidden": true,
		"fa_icon": "fas fa-align-justify",
		"description": "Normalisation constant"
		},
		"igg_control": {
		"type": "boolean",
		"default": true,
		"fa_icon": "fas fa-align-justify",
		"description": "Specifies if the samplesheet contains an IgG control"
		},
		"peak_threshold": {
		"type": "number",
		"default": 0.05,
		"fa_icon": "fas fa-align-justify",
		"description": "Threshold for peak calling when no IgG is present"
		},
		"gene_bed": {
		"type": "string",
		"fa_icon": "fas fa-align-justify",
		"description": "Path to gene bed file"
		},
		"replicate_threshold": {
		"type": "integer",
		"default": 1,
		"fa_icon": "fas fa-align-justify",
		"description": "Minimum number of overlapping replicates needed for a consensus peak"
		}
		},
		"fa_icon": "fas fa-cog"
		},
		"flow_switching_options": {
		"title": "Flow switching options",
		"type": "object",
		"description": "",
		"default": "",
		"properties": {
		"only_genome": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Run pipeline up to reference preparation"
		},
		"only_input": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Run pipeline up to input checking"
		},
		"only_preqc": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Run pipeline up to pre-alignment"
		},
		"only_alignment": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Run pipeline up to alignment"
		},
		"only_filtering": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Run pipeline up to q-filtering"
		},
		"only_peak_calling": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Run pipeline up to peak calling"
		},
		"skip_fastqc": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skips fastqc reporting"
		},
		"skip_trimming": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skips trimming"
		},
		"skip_removeduplicates": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skips de-duplication"
		},
		"skip_scale": {
		"type": "boolean",
		"description": "Skips scalefactor normalisation",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_reporting": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skips reporting"
		},
		"skip_igv": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skips igv session generation"
		},
		"skip_heatmaps": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skips deeptools heatmaps"
		},
		"skip_multiqc": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skips multiqc"
		},
		"skip_upset_plots": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify",
		"description": "Skip upset plot calculation"
		}
		},
		"fa_icon": "fas fa-exchange-alt"
		},
		"institutional_config_options": {
		"title": "Institutional config options",
		"type": "object",
		@@ -256,248 +510,32 @@
		"help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues."
		}
		}
		},
		"trimming_options": {
		"title": "Trimming Options",
		"type": "object",
		"description": "",
		"default": "",
		"properties": {
		"clip_r1": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify"
		},
		"clip_r2": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify"
		},
		"three_prime_clip_r1": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify"
		},
		"three_prime_clip_r2": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify"
		},
		"trim_nextseq": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-align-justify"
		}
		},
		"fa_icon": "fas fa-cut"
		},
		"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"
		],
		"properties": {
		"input": {
		"type": "string",
		"format": "file-path",
		"mimetype": "text/csv",
		"pattern": "^\\S+\\.csv$",
		"schema": "assets/schema_input.json",
		"description": "Path to comma-separated file containing information about the samples in the experiment.",
		"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re//usage#samplesheet-input).",
		"fa_icon": "fas fa-file-csv"
		},
		"outdir": {
		"type": "string",
		"description": "Path to the output directory where the results will be saved.",
		"default": "./results",
		"fa_icon": "fas fa-folder-open"
		},
		"email": {
		"type": "string",
		"description": "Email address for completion summary.",
		"fa_icon": "fas fa-envelope",
		"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
		"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
		},
		"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_reference": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus"
		},
		"save_merged_fastq": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus"
		},
		"save_trimmed": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus"
		},
		"save_spikein_aligned": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus"
		},
		"save_unaligned": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus"
		},
		"save_align_intermed": {
		"type": "boolean",
		"fa_icon": "fas fa-folder-plus"
		},
		"aligner": {
		"type": "string",
		"default": "bowtie2",
		"hidden": true,
		"fa_icon": "fas fa-align-justify"
		}
		}
		},
		"flow_switching_options": {
		"title": "Flow switching options",
		"type": "object",
		"description": "",
		"default": "",
		"properties": {
		"only_genome": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"only_input": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"only_preqc": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"only_alignment": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"only_filtering": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"only_peak_calling": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_fastqc": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_trimming": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_removeduplicates": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_scale": {
		"type": "boolean",
		"description": "Skip scalefactor normalisation",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_reporting": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_igv": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_heatmaps": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_multiqc": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		},
		"skip_upset_plots": {
		"type": "boolean",
		"fa_icon": "fas fa-align-justify"
		}
		},
		"fa_icon": "fas fa-exchange-alt"
		},
		"pipeline_options": {
		"title": "Pipeline Options",
		"type": "object",
		"description": "",
		"default": "",
		"properties": {
		"minimum_alignment_q_score": {
		"type": "integer",
		"default": 0,
		"fa_icon": "fas fa-sort-numeric-down"
		},
		"dedup_target_reads": {
		"type": "boolean",
		"fa_icon": "fas fa-clone"
		},
		"normalisation_c": {
		"type": "integer",
		"default": 10000,
		"hidden": true,
		"fa_icon": "fas fa-align-justify"
		},
		"igg_control": {
		"type": "boolean",
		"default": true,
		"fa_icon": "fas fa-align-justify"
		},
		"peak_threshold": {
		"type": "number",
		"default": 0.05,
		"fa_icon": "fas fa-align-justify"
		},
		"gene_bed": {
		"type": "string",
		"fa_icon": "fas fa-align-justify"
		},
		"replicate_threshold": {
		"type": "integer",
		"default": 1,
		"fa_icon": "fas fa-align-justify"
		}
		},
		"fa_icon": "fas fa-cog"
		}
		},
		"allOf": [
		{
		"$ref": "#/definitions/reference_data_options"
		"$ref": "#/definitions/input_output_options"
		},
		{
		"$ref": "#/definitions/institutional_config_options"
		"$ref": "#/definitions/trimming_options"
		},
		{
		"$ref": "#/definitions/max_job_request_options"
		"$ref": "#/definitions/reference_data_options"
		},
		{
		"$ref": "#/definitions/generic_options"
		"$ref": "#/definitions/pipeline_options"
		},
		{
		"$ref": "#/definitions/trimming_options"
		"$ref": "#/definitions/flow_switching_options"
		},
		{
		"$ref": "#/definitions/input_output_options"
		"$ref": "#/definitions/institutional_config_options"
		},
		{
		"$ref": "#/definitions/flow_switching_options"
		"$ref": "#/definitions/max_job_request_options"
		},
		{
		"$ref": "#/definitions/pipeline_options"
		"$ref": "#/definitions/generic_options"
		}
		]
		}
		No newline at end of file

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