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nextflow_schema.json: Any of --fasta or --genome #471

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[PR #444](https://github.com/nf-core/chipseq/pull/444)] - Add empty map to ch_gff so that when provided by the user `GFFREAD` works.
- [[#451](https://github.com/nf-core/chipseq/issues/451)] - Pass `map.single_read` to `SUBREAD_FEATURECOUNTS` as to correctly set parameter `-p`.
- [[PR #462](https://github.com/nf-core/chipseq/pull/462)] - Updated pipeline template to [nf-core/tools 3.2.1](https://github.com/nf-core/tools/releases/tag/3.2.1)
- Do not require `--fasta` to be set when `--genome` is set.

### Parameters

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108 changes: 87 additions & 21 deletions nextflow_schema.json
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@@ -1,10 +1,10 @@
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/nf-core/chipseq/master/nextflow_schema.json",
"title": "nf-core/chipseq pipeline parameters",
"description": "ChIP-seq peak-calling and differential analysis pipeline.",
"type": "object",
"$defs": {
"definitions": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
Expand Down Expand Up @@ -163,10 +163,10 @@
"igenomes_base": {
"type": "string",
"format": "directory-path",
"description": "The base path to the igenomes reference files",
"fa_icon": "fas fa-ban",
"hidden": true,
"default": "s3://ngi-igenomes/igenomes/"
"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",
Expand All @@ -176,7 +176,14 @@
"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`."
}
},
"required": ["fasta"]
"anyOf": [
{
"required": ["fasta"]
},
{
"required": ["genome"]
}
]
},
"adapter_trimming_options": {
"title": "Adapter trimming options",
Expand Down Expand Up @@ -454,13 +461,54 @@
}
}
},
"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.",
Expand Down Expand Up @@ -550,46 +598,64 @@
"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 warning."
},
"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)."
},
"pipelines_testdata_base_path": {
"type": "string",
"fa_icon": "far fa-check-circle",
"description": "Base URL or local path to location of pipeline test dataset files",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/",
"hidden": true
},
"trace_report_suffix": {
"type": "string",
"fa_icon": "far calendar",
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
"$ref": "#/definitions/input_output_options"
},
{
"$ref": "#/definitions/reference_genome_options"
},
{
"$ref": "#/$defs/adapter_trimming_options"
"$ref": "#/definitions/adapter_trimming_options"
},
{
"$ref": "#/$defs/alignment_options"
"$ref": "#/definitions/alignment_options"
},
{
"$ref": "#/$defs/peak_calling_options"
"$ref": "#/definitions/peak_calling_options"
},
{
"$ref": "#/$defs/process_skipping_options"
"$ref": "#/definitions/process_skipping_options"
},
{
"$ref": "#/$defs/reference_genome_options"
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/$defs/institutional_config_options"
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/$defs/generic_options"
"$ref": "#/definitions/generic_options"
}
]
}