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

Path to tab-separated sample sheet

required
type: string

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

required
type: string

Email address for completion summary.

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

Parameters for QC and trim short-reads

save files that failed to pass trimming thresholds ending in *.fail.fastq.gz

type: boolean

save all merged reads to the a file ending in *.merged.fastq.gz

type: boolean

Skip FastQC

type: boolean

Skip FastP

type: boolean

Path to Kraken2 database.

type: string

Parameters for the assembly

The assembler to use for assembly. Available options are Unicycler, Canu, Miniasm. The latter two are only available for long-read data, whereas Unicycler can be used for short or hybrid assembly projects.

type: string
default: unicycler

Which type of assembly to perform.

type: string
default: short

Extra arguments for Unicycler

type: string

Allowed technologies for long read assembly : [“-pacbio”, “-nanopore”, “-pacbio-hifi”]

type: string

This can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.

type: string

Which assembly polishing method to use.

type: string
default: medaka

Parameters for the annotation

The annotation method to annotate the final assembly. Default choice is prokka, but the dfast tool is also available. For the latter, make sure to create your specific config if you’re not happy with the default one provided. See #dfast_config to find out how.

type: string

Extra arguments for prokka annotation tool.

type: string

Path to Bakta database

type: string

Download Bakta database

type: boolean

This can be used to supply extra options to the Bakta download module

type: string

Specifies a configuration file for the DFAST annotation method.

type: string
default: assets/test_config_dfast.py

Skip running Kraken2 classifier on reads.

type: boolean

Skip annotating the assembly with Prokka /DFAST.

type: boolean

Skip running PycoQC on long read input.

type: boolean

Skip polishing the long-read assembly with fast5 input. Will not affect short/hybrid assemblies.

type: boolean

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

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

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$

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*)+$

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

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

type: string

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})$

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

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

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean

A comma separated string of inputs the schema validation should ignore

hidden
type: string
default: modules,igenomes_base