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

Path to tab-separated sample sheet

required
type: string

Path to sample sheet, either tab-separated (.tsv), comma-separated (.csv), or in YAML format (.yml/.yaml), that points to compressed fastq files.

The sample sheet must have six tab-separated columns/entries with the following headers:

  • ID (required): Unique sample IDs, must start with a letter, and can only contain letters, numbers or underscores
  • R1 (optional): Paths to (forward) reads zipped FastQ files
  • R2 (optional): Paths to reverse reads zipped FastQ files, required if the data is paired-end
  • LongFastQ (optional): Paths to long reads zipped FastQ files
  • Fast5 (optional): Paths to the directory containing FAST5 files
  • GenomeSize (optional): A number (including decimals) ending with 'm', representing genome size.

Please be aware that files will be required based on the chosen assembly type specified with the '--assembly_type' option, which can be set to one of the following values: ['short', 'long', 'hybrid'].`

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})$

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.

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

See Kraken2 homepage for download
links. Minikraken2 8GB is a reasonable choice, since we run Kraken here mainly just to check for
sample purity.

Parameters for the assembly

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

type: string

Which type of assembly to perform.

type: string
default: short

This adjusts the type of assembly done with the input data and can be any of long, short or hybrid. Short & Hybrid assembly will always run Unicycler, whereas long-read assembly can be configured separately using the --assembler parameter.

Extra arguments for Unicycler

type: string

This advanced option allows you to pass extra arguments to Unicycler (e.g. "--mode conservative" or "--no_correct"). For this to work you need to quote the arguments and add at least one space.

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

Extra arguments for Dragonflye

type: string

This advanced option allows you to add extra arguments to Dragonflye (e.g.: "--gsize 2.4m"). For those arguments with no values/options associated (e.g.: "--nopolish" or "--nofilter"...) you need to add an extra space at the begining of the input string to params.dragonflye_args. Example: --params.dragonflye_args ' --nopolish'

Which assembly polishing method to use.

type: string
default: medaka

Can be used to define which polishing method is used by default for long reads. Default is medaka, available options are nanopolish or 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

This advanced option allows you to pass extra arguments to Prokka (e.g. " --rfam" or " --genus name"). For this to work you need to quote the arguments and add at least one space between the arguments. Example:

--prokka_args `--rfam --genus Escherichia Coli`  

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

This can be used instead of PROKKA if required to specify a specific config file for annotation. If you want to know how to create your config file, please refer to the DFAST readme on how to create one. The default config (assets/test_config_dfast.py) is just included for testing, so if you want to annotate using DFAST, you have to create a config!

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

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.

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})$

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.

A comma separated string of inputs the schema validation should ignore

hidden
type: string
default: modules,igenomes_base