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

Path to a sample sheet describing paths to input fastq files

required
type: string

The output directory where the results will be saved.

type: string
default: ./results

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.

Path to a fasta file of the reference sequence

required
type: string

Trim reads

type: boolean
default: true

Saved failed read files after trimminng

type: boolean

path to file containing adapters in fasta format

type: string
default: ${baseDir}/assets/adapters.fas

Turn off subsampling

type: boolean

Desired coverage depth when subsampling

type: integer
default: 100

Specify genome size for subsampling rather than estimation using mash sketch

type: string

Remove recombination using gubbins

type: boolean

Maximum non GATC bases (i.e - and N) to allow in pseudogenome sequences

type: number
default: 0.5

Build a tree using the RapidNJ neighbour-joining algorithm

type: boolean

Build a tree using the FastTree approximate ML algorithm

type: boolean

Build a tree using the IQ-TREE ML algorithm

type: boolean

Build a tree using the RAxML-NG ML algorithm

type: boolean

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

Display help text.

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})$

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

Send plain-text email instead of HTML.

hidden
type: boolean

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

Do not use coloured log outputs.

hidden
type: boolean

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

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.

hidden
type: boolean

NOT USED: File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB

NOT USED: Skip MultiQC

hidden
type: boolean

Custom config file to supply to MultiQC.

hidden
type: string

Custom title for the MultiQC report.

hidden
type: string

enable conda rather than use containers

type: boolean

Boolean whether to validate parameters against the schema at runtime

type: boolean
default: true

Show all params when using --help

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.

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: 4

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: 16.GB
pattern: ^[\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|m|h|d)$

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'

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

Git commit id for Institutional configs.

hidden
type: string
default: master

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

## Download and use config file with following git commit id  
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96  

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 the custom_config_base option. For example:

## Download and unzip the config files  
cd /path/to/my/configs  
wget https://github.com/nf-core/configs/archive/master.zip  
unzip master.zip  
  
## Run the pipeline  
cd /path/to/my/data  
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/  

Note that the nf-core/tools helper package has a download command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.

Institutional configs hostname.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string