Introduction Usage Parameters Output 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.

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

Path to comma-separated file containing information about the reference genomes.

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

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

required
type: string

Options to be provided to the pipeline

Used as a prefix for (merged) output reports

type: string
default: coproid

Path to a kraken2 database, can be a directory or *.tar.gz

required
type: string

Sources TAXID count table in csv format for sourcepredict

required
type: string

Labels for the sources table in csv format for sourcepredict

required
type: string

Path to pre-downloaded ~/.etetoolkit/taxa.sqlite file, if not supplied it will be pulled from the test-data repository

type: string

Path to pre-downloaded ~/.etetoolkit/taxa.sqlite.traverse.pkl file, if not supplied it will be pulled from the test-data repository

type: string

Path to pre-downloaded ~/.sam2lca directory, if not supplied a local database will be build from the reference genomes

type: string

Sam2lca parameter —acc2tax, use default ‘adnamap’ when no sam2lca_db is supplied, change accordingly for sam2lca_db (e.g. ‘nucl’)

type: string
default: adnamap

Set the sam2lca —identity parameter

type: number
default: 0.9

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

Display version and exit.

hidden
type: boolean

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

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

type: string
default: coproid

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.

hidden
type: string

This works exactly as with —email, except emails are only sent if the workflow is not successful.

hidden
type: string

Path to igenomes base

hidden
type: string
default: s3://ngi-igenomes/igenomes/

Boolean whether to ignore igenomes

hidden
type: boolean
default: true

Custom MultiQC yaml file containing HTML including a methods description.

hidden
type: string

Base path to test data.

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

Base path to pipelines data.

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

Name of the config profile.

hidden
type: string

Description of the config profile.

hidden
type: string

Provide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.

hidden
type: string
default: master

Base path to custom config files.

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

Contact of the config profile.

hidden
type: string

URL to config file.

hidden
type: string

Config file for multiQC.

hidden
type: string

Logo for multiQC.

hidden
type: string

Maximum email size.

hidden
type: string
default: 25.MB

Value passed to Nextflow publishDir directive for publishing results in the output directory. Available: ‘symlink’, ‘rellink’, ‘link’, ‘copy’, ‘copyNoFollow’ and ‘move’ (Default: ‘copy’).

hidden
type: string
default: copy

Set to receive plain-text e-mails instead of HTML formatted.

hidden
type: boolean

Set to disable colourful command line output and live life in monochrome.

hidden
type: boolean

Specify YOUR-HOOK-URL to receive notifications from your pipeline in Microsoft Teams or Slack.

hidden
type: string
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