Introduction Usage Parameters Output Results Releases

Define where the pipeline should find input data and save output data.

Path to comma-separated file containing information about the samples in the experiment.

type: string
pattern: ^\S+\.csv$

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.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

type: string

Output intermediate files, including specific prediction lists.

type: boolean
default: false

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

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.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

All options related to the ortholog search subworkflow.

Use all ortholog search methods. Will mix online and local methods if needed. Overrides all individual database flags.

type: boolean
default: false

If set to true, the pipeline will use all ortholog search methods.

Use local databases for the analysis.

type: boolean
default: false

If set to true, the pipeline will use local databases for the analysis.

Run the pipeline in offline mode. Overrides all online database flags.

type: boolean
default: false

If set to true, the pipeline will run in offline mode. local_databases must be set separately.

Skip using OMA for the ortholog search.

type: boolean
default: false

If set to true, the pipeline will not use OMA for the ortholog search.

Path to the OMA database.

type: string

If local_databases is set to true, the pipeline will use this path to the OMA database.

Path to the Uniprot-OMA ID map.

type: string

If local_databases is set to true, the pipeline will use this path to the OMA-Uniprot ID map.

Path to the Ensembl-OMA ID map.

type: string

If local_databases is set to true, the pipeline will use this path to the OMA-Ensembl ID map.

Path to the RefSeq-OMA ID map.

type: string

If local_databases is set to true, the pipeline will use this path to the OMA-RefSeq ID map.

Skip using PANTHER for the ortholog search.

type: boolean
default: false

If set to true, the pipeline will not use PANTHER for the ortholog search.

Path to the PANTHER database.

type: string

If local_databases is set to true, the pipeline will use this path to the PANTHER database.

Skip using OrthoInspector for the ortholog search.

type: boolean
default: false

If set to true, the pipeline will not use OrthoInspector for the ortholog search.

The version of the OrthoInspector database to use.

type: string
default: Eukaryota2023

This SHOULD be left as the default if working with eukaryotes. Only change if working with bacteria, or an old version is required for reproducibility.

Path to the OrthoInspector database.

type: string

If local_databases is set to true, the pipeline will use this path to the OrthoInspector database.

Use EggNOG for the ortholog search.

type: boolean
default: false

If set to true, the pipeline will not use EggNOG for the ortholog search.

Path to the EggNOG database.

type: string

If local_databases is set to true, the pipeline will use this path to the EggNOG database.

Path to the EggNOG ID map.

type: string

If local_databases is set to true, the pipeline will use this path to the EggNOG ID map.

Use centroid strategy for the ortholog search. Overrides min_score.

type: boolean
default: false

If set to true, the pipeline will use centroid strategy for the ortholog search.

Minimum score for the ortholog search.

type: number
default: 2

The minimum score for the ortholog search. If use_centroid is set to true, this parameter will be ignored.

All options related to the downstream analysis subworkflows.

Skip the downstream analysis. Overrides all other downstream options.

type: boolean
default: false

If set to true, the pipeline will skip the downstream analysis.

Skip report generation.

type: boolean
default: false

If set to true, the pipeline will not generate a report. Intended for large batch processing.

Use structures for the analysis.

type: boolean
default: false

If set to true, the pipeline will use AlphaFold structures for the analysis.

Number of bootstrap replicates for IQ-TREE.

type: integer
default: 1000

If set to 0, bootstrap will not be performed.

Number of bootstrap replicates for FastME.

type: integer
default: 100

If set to 0, bootstrap will not be performed.

Options to skip various steps within the workflow.

Skip the ortholog plots.

type: boolean
default: false

If set to true, the pipeline will skip the ortholog plots.

Skip using IQ-TREE for the phylogenetic analysis.

type: boolean
default: false

If set to true, the pipeline will not use IQ-TREE for the phylogenetic analysis.

Skip using FastME for the phylogenetic analysis.

type: boolean
default: false

If set to true, the pipeline will not use FastME for the phylogenetic analysis.

Skip the tree plots.

type: boolean
default: false

If set to true, the pipeline will skip the tree plots.

Skip MultiQC.

type: boolean

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

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.

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

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'

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

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'

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

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 for details.

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

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.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/
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