nextflow_schema.json

{
    "$schema": "https://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/mhcquant/master/nextflow_schema.json",
    "title": "nf-core/mhcquant pipeline parameters",
    "description": "Identify and quantify peptides from mass spectrometry raw data",
    "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",
                    "fa_icon": "fab fa-think-peaks",
                    "description": "Input raw / mzML files listed in a tsv file (see help for details)",
                    "help_text": "Use this to specify a sample sheet table including your input raw or mzml files as well as their metainformation such as SampleID and Condition. For example:\n\n| ID   | Sample      | Condition  |   ReplicateFileName                       |\n| -----|:------------:| ----------:|------------------------------------------:|\n| 1    | MM15_Melanom |      A     |   data/MM15_Melanom_W_1_A_standard.raw    |\n| 2    | MM15_Melanom |      B     |   data/MM15_Melanom_W_1_B_standard.raw    |\n| 3    | MM17_Melanom |      B     |   data/MM17_Melanom_W_1_B_standard.raw    |\n\n```bash\n--input 'path/samples.tsv'\n```"
                },
                "outdir": {
                    "type": "string",
                    "description": "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})$"
                }
            }
        },
        "database_options": {
            "title": "Database Options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "fasta": {
                    "type": "string",
                    "fa_icon": "fas fa-dna",
                    "description": "Input FASTA protein database",
                    "help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
                },
                "inlude_proteins_from_vcf": {
                    "type": "boolean",
                    "description": "Set depending on whether variants should be translated to proteins and included into your fasta for database search."
                },
                "skip_decoy_generation": {
                    "type": "boolean",
                    "description": "Set depending on whether own decoy database should be used",
                    "help_text": "If you want to use your own decoys, you can specify a databaset that includes decoy sequences. However, each database entry should keep the prefix 'DECOY_'.\nOne should consider though that this option will then prevent to append variants to the database and if not using reversed decoys the subset refinement FDR option will not work."
                }
            }
        },
        "preprocessing": {
            "title": "Preprocessing",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "pick_ms_levels": {
                    "type": "integer",
                    "default": 2,
                    "description": "If one ms level in the raw ms data is not centroided, specify the level here. (eg. 2)"
                },
                "run_centroidisation": {
                    "type": "boolean",
                    "description": "Choose whether the specified ms_level in pick_ms_levels is centroided or not."
                }
            }
        },
        "mass_spectrometry_data_processing": {
            "title": "Mass Spectrometry Data Processing",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "peptide_min_length": {
                    "type": "integer",
                    "default": 8,
                    "description": "Specify the minimum length of peptides considered after processing"
                },
                "peptide_max_length": {
                    "type": "integer",
                    "default": 12,
                    "description": "Specify the maximum length of peptides considered after processing"
                },
                "fragment_mass_tolerance": {
                    "type": "number",
                    "default": 0.02,
                    "description": "Specify the fragment mass tolerance used for the comet database search.",
                    "help_text": "For High-Resolution instruments a fragment mass tolerance value of 0.02 is recommended. (See the Comet parameter documentation: eg. 0.02)"
                },
                "precursor_mass_tolerance": {
                    "type": "integer",
                    "default": 5,
                    "description": "Specify the precursor mass tolerance used for the comet database search.",
                    "help_text": " For High-Resolution instruments a precursor mass tolerance value of 5ppm is recommended. (eg. 5)"
                },
                "fragment_bin_offset": {
                    "type": "integer",
                    "description": "Specify the fragment bin offset used for the comet database search.",
                    "help_text": "For High-Resolution instruments a fragment bin offset of 0 is recommended. (See the Comet parameter documentation: eg. 0)"
                },
                "number_mods": {
                    "type": "integer",
                    "default": 3,
                    "description": "Specify the maximum number of modifications that should be contained in a peptide sequence match."
                },
                "num_hits": {
                    "type": "integer",
                    "default": 1,
                    "description": "Specify the number of hits that should be reported for each spectrum."
                },
                "digest_mass_range": {
                    "type": "string",
                    "default": "800:2500",
                    "description": "Specify the mass range that peptides should fullfill to be considered for peptide spectrum matching."
                },
                "prec_charge": {
                    "type": "string",
                    "default": "2:3",
                    "description": "Specifiy the precursor charge range that peptides should fullfill to be considered for peptide spectrum matching."
                },
                "activation_method": {
                    "type": "string",
                    "default": "ALL",
                    "description": "Specify which fragmentation method was used in the MS acquisition",
                    "enum": [
                        "ALL",
                        "CID",
                        "ECD",
                        "ETD",
                        "PQD",
                        "HCD",
                        "IRMPD"
                    ]
                },
                "enzyme": {
                    "type": "string",
                    "default": "unspecific cleavage",
                    "description": "Specify which enzymatic restriction should be applied",
                    "hidden": true,
                    "help_text": " for HLA peptides rarely other enzymes are used, however most enzymes such as for example 'Trypsin' are available (see OpenMS enzymes)"
                },
                "max_rt_alignment_shift": {
                    "type": "integer",
                    "default": 300,
                    "description": "Set a maximum retention time shift for the linear rt alignment"
                },
                "fixed_mods": {
                    "type": "string",
                    "description": "Specify which fixed modifications should be applied to the database search",
                    "help_text": "e.g. 'Carbamidomethyl (C)' (see OpenMS modifications)"
                },
                "variable_mods": {
                    "type": "string",
                    "default": "Oxidation (M)",
                    "description": "Specify which variable modifications should be applied to the database search",
                    "help_text": "e.g. 'Oxidation (M)' (see OpenMS modifications)"
                },
                "use_x_ions": {
                    "type": "boolean",
                    "description": "Include x ions into the peptide spectrum matching"
                },
                "use_z_ions": {
                    "type": "boolean",
                    "description": "Include z ions into the peptide spectrum matching"
                },
                "use_a_ions": {
                    "type": "boolean",
                    "description": "Include a ions into the peptide spectrum matching"
                },
                "use_c_ions": {
                    "type": "boolean",
                    "description": "Include c ions into the peptide spectrum matching"
                },
                "use_NL_ions": {
                    "type": "boolean",
                    "description": "Include NL ions into the peptide spectrum matching"
                },
                "remove_precursor_peak": {
                    "type": "boolean",
                    "description": "Include precursor ions into the peptide spectrum matching",
                    "default": true
                },
                "spectrum_batch_size": {
                    "type": "integer",
                    "default": 500,
                    "description": "Size of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)"
                },
                "vcf_sheet": {
                    "type": "string",
                    "description": "Specify a .tsv file containing the information about genomic variants (vcf files < v.4.2) for each sample.",
                    "help_text": "| Sample      | VCF_FileName           |\n| -------------| :---------------------:|\n| MM15_Melanom | data/MM15_variants.vcf |\n| MM17_Melanom | data/MM17_variants.vcf |"
                }
            }
        },
        "fdr_scoring": {
            "title": "FDR Scoring",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "fdr_level": {
                    "type": "string",
                    "default": "peptide-level-fdrs",
                    "description": "Specify the level at which the false discovery rate should be computed.",
                    "enum": [
                        "peptide-level-fdrs",
                        "psm-level-fdrs",
                        "protein-level-fdrs"
                    ]
                },
                "fdr_threshold": {
                    "type": "number",
                    "default": 0.01,
                    "description": "Specify the false discovery rate threshold at which peptide hits should be selected."
                },
                "refine_fdr_on_predicted_subset": {
                    "type": "boolean",
                    "help_text": "SubsetFDR makes use of binding predictions applying the tool mhcflurry to subset all PSMs not passing the q-value threshold. If specified the FDR will be refined using Percolator on the subset of predicted binders among all PSMs resulting in an increased identification rate. (Please be aware that this option is only available for MHC class I data of alleles that are supported by mhcflurry)",
                    "description": "Set if MHCquant should be run in SubsetFDR mode"
                },
                "subset_affinity_threshold": {
                    "type": "integer",
                    "default": "500",
                    "description": "Affinity threshold (nM) used to define binders for PSM subset selection in the FDR refinement procedure"
                },
                "description_correct_features": {
                    "type": "integer",
                    "description": "Specify percolator descriptor feature set",
                    "help_text": "See percolator description (https://github.com/percolator/percolator/wiki/Retention-time-and-calibration)"
                },
                "klammer": {
                    "type": "boolean",
                    "description": "Use klammer retention time features for Percolator rescoring",
                    "help_text": "https://pubs.acs.org/doi/10.1021/ac070262k"
                },
                "subset_max_train": {
                    "type": "integer",
                    "description": "Maximum subset for percolator training iterations"
                }
            }
        },
        "quantification_options": {
            "title": "Quantification Options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "skip_quantification": {
                    "type": "boolean",
                    "description": "Skip quantification and only yield peptide identifications"
                },
                "quantification_fdr": {
                    "type": "string",
                    "description": "Compute FDR for the targeted approach",
                    "help_text": "(Weisser H. and Choudhary J.S. J Proteome Res. 2017 Aug 4)"
                },
                "quantification_min_prob": {
                    "type": "number",
                    "description": "Specify a cut off probability value for quantification events as a filter"
                }
            }
        },
        "mhc_affinity_prediction": {
            "title": "MHC affinity prediction",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "allele_sheet": {
                    "type": "string",
                    "description": "Specify a .tsv file containing the MHC alleles of your probes as well as their metadata such as SampleID.",
                    "help_text": "| Sample      | HLA_Alleles_Class_1                             | HLA_Alleles_Class_2                        |\n| -------------| :----------------------------------------------:| ------------------------------------------:|\n| MM15_Melanom | A* 03:01;A* 68:01;B* 27:05;B* 35:03;C* 02:02;C* 04:01 |HLA-DRB1* 01:01;HLA-DQB1* 03:19;HLA-DQA1* 05:01|\n| MM17_Melanom | A* 02:01;B* 07:01;B* 26:01;C* 11:01;C* 01:01         |HLA-DRB1* 01:02;HLA-DRB3* 02:02;HLA-DRB4* 01:03|\n"
                },
                "predict_class_1": {
                    "type": "boolean",
                    "description": "Set flag depending on whether MHC class 1 binding predictions using the tool mhcflurry should be run."
                },
                "predict_class_2": {
                    "type": "boolean",
                    "description": "Set flag depending on whether MHC class 2 binding predictions using the tool mhcnuggets should be run."
                }
            }
        },
        "variant_options": {
            "title": "Variant Options",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "variant_reference": {
                    "type": "string",
                    "description": "Specify genomic reference used for variant annotation",
                    "enum": [
                        "GRCH37",
                        "GRCH38"
                    ],
                    "default": "GRCH38"
                },
                "variant_annotation_style": {
                    "type": "string",
                    "description": "Specify style of tool used for variant annotation - currently supported",
                    "enum": [
                        "SNPEFF",
                        "VEP",
                        "ANNOVAR"
                    ],
                    "default": "SNPEFF"
                },
                "variant_indel_filter": {
                    "type": "boolean",
                    "description": "Specify whether insertions and deletions should not be considered for variant translation",
                    "default": true
                },
                "variant_frameshift_filter": {
                    "type": "boolean",
                    "description": "Specify whether frameshifts should not be considered for variant translation",
                    "default": true
                },
                "variant_snp_filter": {
                    "type": "boolean",
                    "description": "Specify whether snps should not be considered for variant translation"
                }
            }
        },
        "rt_prediction": {
            "title": "RT Prediction",
            "type": "object",
            "description": "",
            "default": "",
            "properties": {
                "predict_RT": {
                    "type": "boolean",
                    "description": "Set this option to predict retention times of all identified peptides and possible neoepitopes based on high scoring ids"
                }
            }
        },
        "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.",
                    "hidden": true,
                    "fa_icon": "fas fa-question-circle"
                },
                "publish_dir_mode": {
                    "type": "string",
                    "default": "copy",
                    "hidden": true,
                    "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",
                        "mov"
                    ]
                },
                "name": {
                    "type": "string",
                    "description": "Workflow name.",
                    "fa_icon": "fas fa-fingerprint",
                    "hidden": true,
                    "help_text": "A custom name for the pipeline run. Unlike the core nextflow `-name` option with one hyphen this parameter can be reused multiple times, for example if using `-resume`. Passed through to steps such as MultiQC and used for things like report filenames and titles."
                },
                "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})$",
                    "hidden": true,
                    "help_text": "This works exactly as with `--email`, except emails are only sent if the workflow is not successful."
                },
                "plaintext_email": {
                    "type": "boolean",
                    "description": "Send plain-text email instead of HTML.",
                    "fa_icon": "fas fa-remove-format",
                    "hidden": true,
                    "help_text": "Set to receive plain-text e-mails instead of HTML formatted."
                },
                "monochrome_logs": {
                    "type": "boolean",
                    "description": "Do not use coloured log outputs.",
                    "fa_icon": "fas fa-palette",
                    "hidden": true,
                    "help_text": "Set to disable colourful command line output and live life in monochrome."
                },
                "tracedir": {
                    "type": "string",
                    "description": "Directory to keep pipeline Nextflow logs and reports.",
                    "default": "${params.outdir}/pipeline_info",
                    "fa_icon": "fas fa-cogs",
                    "hidden": true
                }
            }
        },
        "reference_genome_options": {
            "title": "Reference genome options",
            "type": "object",
            "fa_icon": "fas fa-dna",
            "description": "Options for the reference genome indices used to align reads.",
            "properties": {
                "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`."
                }
            }
        },
        "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",
                    "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",
                    "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'`"
                }
            }
        },
        "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",
                    "help_text": "Provide git commit id for custom Institutional configs hosted at `nf-core/configs`. This was implemented for reproducibility purposes. Default: `master`.\n\n```bash\n## Download and use config file with following git commit id\n--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96\n```"
                },
                "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 the `custom_config_base` option. For example:\n\n```bash\n## Download and unzip the config files\ncd /path/to/my/configs\nwget https://github.com/nf-core/configs/archive/master.zip\nunzip master.zip\n\n## Run the pipeline\ncd /path/to/my/data\nnextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/\n```\n\n> Note that the nf-core/tools helper package has a `download` command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.",
                    "fa_icon": "fas fa-users-cog"
                },
                "hostnames": {
                    "type": "string",
                    "description": "Institutional configs hostname.",
                    "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"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_options"
        },
        {
            "$ref": "#/definitions/database_options"
        },
        {
            "$ref": "#/definitions/preprocessing"
        },
        {
            "$ref": "#/definitions/mass_spectrometry_data_processing"
        },
        {
            "$ref": "#/definitions/fdr_scoring"
        },
        {
            "$ref": "#/definitions/quantification_options"
        },
        {
            "$ref": "#/definitions/mhc_affinity_prediction"
        },
        {
            "$ref": "#/definitions/variant_options"
        },
        {
            "$ref": "#/definitions/rt_prediction"
        },
        {
            "$ref": "#/definitions/generic_options"
        },
        {
            "$ref": "#/definitions/reference_genome_options"
        },
        {
            "$ref": "#/definitions/max_job_request_options"
        },
        {
            "$ref": "#/definitions/institutional_config_options"
        }
    ],
    "properties": {
        "clusterOptions": {
            "type": "string"
        },
        "awsqueue": {
            "type": "string"
        },
        "awsregion": {
            "type": "string",
            "default": "eu-west-1"
        },
        "include_proteins_from_vcf": {
            "type": "string"
        },
        "config_profile_name": {
            "type": "string",
            "default": "Full test profile"
        },
        "igenomes_base": {
            "type": "string",
            "default": "s3://ngi-igenomes/igenomes/"
        },
        "multiqc_config": {
            "type": "string"
        }
    }
}