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{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"$id": "https://raw.githubusercontent.com/CCBR/CRISPIN//nextflow_schema.json",
"title": "CCBR/CRISPIN pipeline parameters",
"description": "CRISPR screen pipeline",
"type": "object",
"$defs": {
"input_output_options": {
"title": "Input/output options",
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"exists": true,
"mimetype": "text/csv",
"pattern": "^\\S+\\.csv$",
"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.",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
"fa_icon": "fas fa-folder-open",
"default": "results"
},
"library": {
"type": "string",
"fa_icon": "fas fa-file-csv"
},
"exp_name": {
"type": "string",
"default": "crispin"
},
"count_table": {
"type": "string",
"fa_icon": "fas fa-file-csv"
},
"design_matrix": {
"type": "string",
"fa_icon": "fas fa-file-alt"
}
}
},
"general_options": {
"title": "General options",
"type": "object",
"description": "",
"default": "",
"properties": {
"publish_dir_mode": {
"type": "string",
"default": "link"
},
"max_memory": {
"type": "string",
"default": "224 GB"
},
"max_cpus": {
"type": "integer",
"default": 32
},
"max_time": {
"type": "string",
"default": "72 h"
},
"index_dir": {
"type": "string",
"fa_icon": "fas fa-folder",
"hidden": true
}
}
},
"trimming_options": {
"title": "Trimming options",
"type": "object",
"description": "",
"default": "",
"properties": {
"cutadapt_adapters": {
"type": "string",
"default": "/opt2/TruSeq_and_nextera_adapters.consolidated.fa",
"fa_icon": "fas fa-file",
"hidden": true
},
"cutadapt_minlen": {
"type": "integer",
"default": 20
},
"cutadapt_leadingquality": {
"type": "integer",
"default": 10
},
"cutadapt_trailingquality": {
"type": "integer",
"default": 10
}
}
},
"control_whether_these_steps_are_executed": {
"title": "Control whether these steps are executed",
"type": "object",
"description": "",
"default": "",
"properties": {
"mageck_run": {
"type": "boolean",
"default": true
},
"drugz_run": {
"type": "boolean",
"default": true
},
"bagel_run": {
"type": "boolean",
"default": true
}
}
},
"crispr_options": {
"title": "crispr options",
"type": "object",
"description": "",
"default": "",
"properties": {
"drugz_remove_genes": {
"type": "string",
"description": "comma-sep str"
},
"drugz_half_window_size": {
"type": "integer",
"default": 500
},
"bagel_core_essential_genes": {
"type": "string",
"default": "/opt2/bagel-2.0-115/CEGv2.txt",
"fa_icon": "fas fa-file"
},
"bagel_non_essential_genes": {
"type": "string",
"default": "/opt2/bagel-2.0-115/NEGv1.txt",
"fa_icon": "fas fa-file"
},
"bagel_test_columns": {
"type": "string"
}
}
},
"docker_containers": {
"title": "Docker containers",
"type": "object",
"description": "",
"default": "",
"properties": {
"container_bagel": {
"type": "string",
"default": "nciccbr/crispin_bagel_2.0:0.1.0"
},
"container_base": {
"type": "string",
"default": "nciccbr/ccbr_ubuntu_base_20.04:v5"
},
"container_cutadapt": {
"type": "string",
"default": "nciccbr/ncigb_cutadapt_v1.18:latest"
},
"container_drugz": {
"type": "string",
"default": "nciccbr/crispin_drugz:0.1.0"
},
"container_mageck": {
"type": "string",
"default": "quay.io/biocontainers/mageck:0.5.9.5--py39h1f90b4d_3"
},
"container_fastqc": {
"type": "string",
"default": "nciccbr/ccrgb_qctools:v4.0"
},
"container_vispr": {
"type": "string",
"default": "quay.io/biocontainers/mageck-vispr:0.5.6--py_0"
}
}
}
},
"allOf": [
{
"$ref": "#/$defs/input_output_options"
},
{
"$ref": "#/$defs/general_options"
},
{
"$ref": "#/$defs/trimming_options"
},
{
"$ref": "#/$defs/control_whether_these_steps_are_executed"
},
{
"$ref": "#/$defs/crispr_options"
},
{
"$ref": "#/$defs/docker_containers"
}
],
"properties": {
"config_profile_name": {
"type": "string",
"hidden": true
},
"config_profile_description": {
"type": "string",
"hidden": true
},
"config_profile_url": {
"type": "string",
"hidden": true
},
"config_profile_contact": {
"type": "string",
"hidden": true
},
"igenomes_base": {
"type": "string",
"hidden": true
}
}
}