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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://github.com/hukai916/scATACpipe/blob/main/nextflow_schema.json",
"title": "Parameters for scATACpipe",
"description": "A Nextflow pipeline for scATACseq data analysis.",
"type": "object",
"definitions": {
"basic_options": {
"title": "Basic options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define output related options",
"properties": {
"help": {
"type": "string",
"description": "Print help info."
},
"outdir": {
"type": "string",
"description": "Path to the output directory where the results will be saved.",
"default": "./results",
"fa_icon": "fas fa-folder-open"
},
"support_genome": {
"type": "string",
"description": "Use this flag to view currently supported genomes."
}
}
},
"input_fragment_option1": {
"title": "Input fragments [option 1: using UCSC/ENSEMBL genome]",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Defines required parameters if input fragment files.",
"properties": {
"input_fragment": {
"type": "string",
"description": "Path to input sample sheet for fragment files.",
"fa_icon": "fas fa-arrow-circle-right"
},
"archr_genome": {
"type": "string",
"description": "A genome name, either ENSEMBL style (e.g. homo_sapiens) or UCSC style (e.g. mm10)."
},
"species_latin_name": {
"type": "string",
"description": "Must be quoted. Required if '--archr_genome' not in (mm9, mm10, hg19, hg38)"
},
"archr_blacklist": {
"type": "string",
"description": "Optional. Path to blacklist file."
}
}
},
"input_fragment_option2": {
"title": "Input fragments [option 2: using custom genome]",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Defines required parameters if input fragment files.",
"properties": {
"input_fragment": {
"type": "string",
"description": "Path to input sample sheet for fragment files.",
"fa_icon": "fas fa-arrow-circle-right"
},
"archr_genome_fasta": {
"type": "string",
"description": "Path to genome fasta."
},
"ref_gtf": {
"type": "string",
"description": "Path to gtf file."
},
"species_latin_name": {
"type": "string",
"description": "Must be quoted."
},
"archr_blacklist": {
"type": "string",
"description": "Optional. Path to blacklist file."
}
}
},
"input_fragment_option3": {
"title": "Input fragments [option 3: using Bioconductor objects]",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Defines required parameters if input fragment files.",
"properties": {
"input_fragment": {
"type": "string",
"description": "Path to input sample sheet for fragment files.",
"fa_icon": "fas fa-arrow-circle-right"
},
"archr_bsgenome": {
"type": "string",
"description": "A Bioconductor BSgenome package name."
},
"archr_txdb": {
"type": "string",
"description": "A Bioconductor TxDb package name."
},
"archr_org": {
"type": "string",
"description": "A Bioconductor OrgDb package name."
},
"archr_blacklist": {
"type": "string",
"description": "Optional. Path to blacklist file."
}
}
},
"input_fastq_option1": {
"title": "Input FASTQs [option 1: using UCSC/ENSEMBL genome]",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Defines required parameters if input fragment files.",
"properties": {
"input_fastq": {
"type": "string",
"description": "Path to input sample sheet for FASTQ files.",
"fa_icon": "fas fa-arrow-circle-right"
},
"preprocess": {
"type": "string",
"description": "Preprocessing method. Choose from 'default', '10xgenomics', 'chromap'.",
"fa_icon": "fas fa-arrow-circle-right"
},
"ref_fasta_ensembl": {
"type": "string",
"description": "A genome name from ENSEMBL (e.g. homo_sapiens)."
},
"ref_fasta_ucsc": {
"type": "string",
"description": "A genome name from UCSC (e.g. mm10)."
},
"mapper": {
"type": "string",
"description": "For '--preprocess default' only. Choose from 'bwa', 'bowtie2(todo)'.",
"default": "bwa"
},
"barcode_whitelist": {
"type": "string",
"description": "For '--preprocess default' only. Path to whitelist folder.",
"default": "./assets/whitelist_barcodes"
},
"barcode_correction": {
"type": "string",
"description": "For '--preprocess default' only. Choose from 'naive', 'pheniqs', and false.",
"default": "pheniqs"
},
"species_latin_name": {
"type": "string",
"description": "Must be quoted."
},
"archr_blacklist": {
"type": "string",
"description": "Optional. Path to blacklist file."
}
}
},
"input_fastq_option2": {
"title": "Input FASTQs [option 2: using custom genome]",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Defines required parameters if input fragment files.",
"properties": {
"input_fastq": {
"type": "string",
"description": "Path to input sample sheet for FASTQ files.",
"fa_icon": "fas fa-arrow-circle-right"
},
"preprocess": {
"type": "string",
"description": "Preprocessing method. Choose from 'default', '10xgenomics', 'chromap'.",
"fa_icon": "fas fa-arrow-circle-right"
},
"ref_fasta": {
"type": "string",
"description": "Path to reference genome file."
},
"ref_gtf": {
"type": "string",
"description": "Path to reference gtf file."
},
"mapper": {
"type": "string",
"description": "For '--preprocess default' only. Choose from 'bwa', 'bowtie2(todo)'.",
"default": "bwa"
},
"whitelist_barcode": {
"type": "string",
"description": "For '--preprocess default' only. Path to whitelist folder.",
"default": "./assets/whitelist_barcodes"
},
"barcode_correction": {
"type": "string",
"description": "For '--preprocess default' only. Choose from 'naive', 'pheniqs', and false.",
"default": "pheniqs"
},
"species_latin_name": {
"type": "string",
"description": "Must be quoted."
},
"archr_blacklist": {
"type": "string",
"description": "Optional. Path to blacklist file."
}
}
},
"input_fastq_option3": {
"title": "Input FASTQs [option 3: using existing genome index]",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Defines required parameters if input fragment files.",
"properties": {
"input_fastq": {
"type": "string",
"description": "Path to input sample sheet for FASTQ files.",
"fa_icon": "fas fa-arrow-circle-right"
},
"preprocess": {
"type": "string",
"description": "Preprocessing method. Choose from 'default', '10xgenomics', 'chromap'.",
"fa_icon": "fas fa-arrow-circle-right"
},
"ref_bwa_index": {
"type": "string",
"description": "For '--preprocess default' only. Path to BWA index folder."
},
"ref_cellranger_index": {
"type": "string",
"description": "For '--preprocess 10xgenomics' only. Path to Cellranger index folder."
},
"ref_chromap_index": {
"type": "string",
"description": "For '--preprocess chromap' only. Path to Chromap index folder."
},
"ref_gtf": {
"type": "string",
"description": "Path to reference gtf file."
},
"mapper": {
"type": "string",
"description": "For '--preprocess default' only. Choose from 'bwa', 'bowtie2(todo)'.",
"default": "bwa"
},
"barcode_whitelist": {
"type": "string",
"description": "For '--preprocess default' only. Path to whitelist folder.",
"default": "./assets/whitelist_barcodes"
},
"barcode_correction": {
"type": "string",
"description": "For '--preprocess default' only. Choose from 'naive', 'pheniqs', and false.",
"default": "pheniqs"
},
"species_latin_name": {
"type": "string",
"description": "Must be quoted."
},
"archr_blacklist": {
"type": "string",
"description": "Optional. Path to blacklist file."
}
}
},
"other_parameters": {
"title": "Other pipeline parameters",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Defines other pipeline related parameters.",
"properties": {
"split_fastq": {
"type": "string",
"description": "Whether or not to split fastq into smaller chunks.",
"default": "false"
},
"read1_adapter": {
"type": "string",
"description": "For trimming read1.",
"default": "AGATCGGAAGAGC"
},
"read2_adapter": {
"type": "string",
"description": "For trimming read2.",
"default": "AGATCGGAAGAGC"
},
"filter": {
"type": "string",
"description": "Method for filtering bam file. Choose from 'both', 'improper', or false to skip.",
"default": "both"
},
"doublet_removal_algorithm": {
"type": "string",
"description": "Method for doublet removel. Choose from 'amulet', 'archr', or false to skip.",
"default": "archr"
},
"archr_batch_correction_harmony": {
"type": "boolean",
"description": "Whether or not to perform batch correction with Harmony",
"default": true
},
"amulet_rmsk_bed": {
"type": "string",
"description": "For '--doublet_removal_algorithm amulet' only. Path to bed file containing repeat regions."
},
"amulet_autosomes": {
"type": "string",
"description": "For '--doublet_removal_algorithm amulet' only. Path to text file containing autosomal chromosome names."
},
"archr_thread": {
"type": "integer",
"description": "Number of threads used for ArchR.",
"default": 4
},
"archr_scrnaseq": {
"type": "string",
"description": "Whether or not to integrate scRNA-seq data. Path to matching scRNAseq Seurat object.",
"default": false
},
"archr_scrnaseq_grouplist": {
"type": "string",
"description": "scRNA-seq cluster grouping info for constrained integration. Example see conf/test_chromap.config.",
"default": false
},
"filter_seurat_ilsi": {
"type": "string",
"description": "Clusters to exclude for downstream analysis. Example see conf/test_chromap.config.",
"default": false
},
"filter_seurat_harmony": {
"type": "string",
"description": "Clusters to exclude for downstream analysis. Example see conf/test_chromap.config.",
"default": false
},
"filter_sample": {
"type": "string",
"description": "Samples to skip for downstream analyses. Example see conf/test_chromap.config.",
"default": false
},
"outlier_further": {
"type": "boolean",
"description": "Set to false to stop immediately after embedding step for outlier detection",
"default": true,
"hidden": true
},
"custom_peaks": {
"type": "string",
"description": "For motif enrichment/deviation. Example see conf/test_chromap.config.",
"hidden": true
}
}
},
"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"
},
"hostnames": {
"type": "string",
"description": "Institutional configs hostname.",
"hidden": true,
"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$",
"hidden": true,
"help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`"
},
"max_time": {
"type": "string",
"description": "Maximum amount of time that can be requested for any single job.",
"default": "240.h",
"fa_icon": "far fa-clock",
"pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
"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
},
"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
},
"multiqc_config": {
"type": "string",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"tracedir": {
"type": "string",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${params.outdir}/pipeline_info",
"fa_icon": "fas fa-cogs",
"hidden": true
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
"fa_icon": "fas fa-check-square",
"hidden": true
},
"show_hidden_params": {
"type": "boolean",
"fa_icon": "far fa-eye-slash",
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"enable_conda": {
"type": "boolean",
"description": "Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter.",
"hidden": true,
"fa_icon": "fas fa-bacon"
},
"singularity_pull_docker_container": {
"type": "boolean",
"description": "Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.",
"hidden": true,
"fa_icon": "fas fa-toolbox",
"help_text": "This may be useful for example if you are unable to directly pull Singularity containers to run the pipeline due to http/https proxy issues."
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/basic_options"
},
{
"$ref": "#/definitions/input_fragment_option1"
},
{
"$ref": "#/definitions/input_fragment_option2"
},
{
"$ref": "#/definitions/input_fragment_option3"
},
{
"$ref": "#/definitions/input_fastq_option1"
},
{
"$ref": "#/definitions/input_fastq_option2"
},
{
"$ref": "#/definitions/input_fastq_option3"
},
{
"$ref": "#/definitions/other_parameters"
},
{
"$ref": "#/definitions/institutional_config_options"
},
{
"$ref": "#/definitions/max_job_request_options"
},
{
"$ref": "#/definitions/generic_options"
}
]
}