phyloplace/nextflow_schema.json at master · nf-core/phyloplace · GitHub - github.com

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{
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://raw.githubusercontent.com/nf-core/phyloplace/master/nextflow_schema.json",
    "title": "nf-core/phyloplace pipeline parameters",
    "description": "Performs phylogenetic placement with EPA-NG",
    "type": "object",
    "$defs": {
        "input_output_options": {
            "title": "Input/output options",
            "type": "object",
            "fa_icon": "fas fa-terminal",
            "description": "Define where the pipeline should find input data and save output data.",
            "required": ["outdir"],
            "properties": {
                "phyloplace_input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_phyloplace_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about phylogenetic placements to perform.",
                    "help_text": "This specifies parameters for direct phylogenetic placement of query sequences onto a reference phylogeny, in contrast to when a HMMER search is first performed, see `--phylosearch_input`. It has to be a comma-separated file with at least five columns, and a header row ('sample', 'queryseqfile', 'refseqfile', 'refphylogeny' and 'model'). See [usage docs](https://nf-co.re/phyloplace/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "phylosearch_input": {
                    "type": "string",
                    "format": "file-path",
                    "exists": true,
                    "schema": "assets/schema_phylosearch_input.json",
                    "mimetype": "text/csv",
                    "pattern": "^\\S+\\.csv$",
                    "description": "Path to comma-separated file containing information about phylogenetic searches to perform.",
                    "help_text": "This specifies parameters for phylogenetic placement of unknown sequences onto reference phylogeny after first using HMMER to search through a collection of uknown sequences (see `--search_fasta`) in contrast to when only placing known query sequences, see `--phyloplace_input`. It has to be a comma-separated file with at least two columns that specifies search HMM profiles ('target' and 'hmm') and at least three columns specifying the reference phylogenies ('refseqfile', 'refphylogeny' and 'model') for placement of search results. (Decoy profiles, i.e. profiles only used for searches, not placements, are allowed.) See [usage docs](https://nf-co.re/phyloplace/usage#samplesheet-input).",
                    "fa_icon": "fas fa-file-csv"
                },
                "search_fasta": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "description": "Fasta file with sequences to be searched with HMM profiles.",
                    "help_text": "Sequences from this file matching an HMM profile, will be placed in the reference phylogeny corresponding to the HMM profile.",
                    "fa_icon": "fas fa-file-tsv"
                },
                "id": {
                    "type": "string",
                    "description": "Name of analysis",
                    "default": "placement",
                    "fa_icon": "fas fa-barcode"
                },
                "alignmethod": {
                    "type": "string",
                    "description": "Method used to align query sequences with.",
                    "help_text": "Query sequences will be aligned to the reference alignment using either HMMER, Clustal Omega or MAFFT, except when an hmm profile is provided (--hmmfile; implies that --alignmethod is set to 'hmmer'), in which case both the reference and query sequences will be aligned with the profile (reference sequences must not be aligned, i.e. must not contain '-' characters).",
                    "default": "hmmer",
                    "fa_icon": "far fa-file-code",
                    "enum": ["hmmer", "clustalo", "mafft"]
                },
                "queryseqfile": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "description": "Fasta file with query sequences",
                    "fa_icon": "far fa-file-code"
                },
                "refseqfile": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "description": "File with reference sequences. Any format supported by HMMER tools.",
                    "help_text": "If the sequences are not aligned, you need to provide an alignment option, e.g. --hmmfile.",
                    "fa_icon": "far fa-file-code"
                },
                "hmmfile": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "description": "HMM file. If provided, will be used to align both the reference and query sequences.",
                    "fa_icon": "far fa-file-code"
                },
                "refphylogeny": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/plain",
                    "description": "Newick file with aligned reference sequences.",
                    "fa_icon": "far fa-file-code"
                },
                "model": {
                    "type": "string",
                    "description": "Evolutionary model to use for placement, e.g. 'LG'.",
                    "fa_icon": "fas fa-barcode"
                },
                "taxonomy": {
                    "type": "string",
                    "format": "file-path",
                    "mimetype": "text/tab-separated-values",
                    "pattern": "^\\S+\\.tsv$",
                    "description": "Tab-separated file with taxonomy assignments of reference sequences.",
                    "help_text": "The first column should consist of names of reference sequences, the second of taxonomy strings, e.g. 'Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia;Escherichia coli'.",
                    "fa_icon": "fas fa-file-tsv"
                },
                "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"
                }
            }
        },
        "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"
                },
                "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"
                }
            }
        },
        "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"
                },
                "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://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": "#/$defs/institutional_config_options"
        },
        {
            "$ref": "#/$defs/generic_options"
        }
    ]
}