Parameters which control the workflow.

If the filtering step should be carried out.

type: boolean

If set to True the filter is used. Otherwise only assessing is performed.

If the pre-processed reads should be used by the filter.

type: boolean

If set to True the the pre-proccesed reads are used for filtering. Else the raw reads are used.

If blastn should be skipped.

type: boolean

Defines if blastn should be used or not. By default blastn is used in the workflow. If also the filter is enabled the reads are filtered using the output from blastn.

If the output of kraken2 should be used for filtering.

type: boolean

If this is set to True the kraken2 output is used for filtering.

Parameters used by kraken2 to classify all reads provided. Fine-tuning of the isolation step can be done via the cutoff_* parameters. The taxon for assessing/filtering can be set using tax2filter.

The database which is used in the classification step.

type: string
default: https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08gb_20231009.tar.gz

For input how to use this parameter to fine-tune the step refer to usage/Databases/kraken2

If the unclassified and classified (only if the reads were classified as any taxon or not, not to confuse with the classification for the assessing/filtering) reads should be saved to different files.

hidden
type: boolean

Confidence in the classification of a read as a certain taxon.

type: number
default: 0.05

Refer to https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#confidence-scoring for details.

If a read has less k-mers assigned to the taxon/taxa to be assessed/to be filtered the read is ignored by the pipeline.

type: integer
default: 2

If the ratio of the sum of k-mers mapped to the taxon/taxa to be assessed/to be filtered to unclassified is below this threshold the read is ignored by the pipeline. Can take values between 0.0 and 1.0.

type: number

The taxon or taxonomic group to be assessed or filtered by the pipeline.

type: string
default: Homo

If a whole taxonomic group should be assessed/filtered use the highest taxonomic name in the hierarchy. E.g. if you want to assess for/filter out the whole taxonomic subtree from Mammalia onward provide this parameter with the string 'Mammalia'.

Parameters to fine-tune the output of blastn.

Coverage is the percentage of the query sequence which can be found in the alignments of the sequence match. It can be used to fine-tune the validation step.

type: number
default: 40

The expected(e)-value contains information on how many hits of the same score can be found in a database of the size used in the query by chance. The parameter can be used to fine-tune the validation step.

type: number
default: 0.01

Identity is the percentage of the exact matches in the query and the sequence found in the database. The parameter can be used to fine-tune the validation step.

type: number
default: 40

Quality control of raw reads.

Can be used to save the output from FastQC to the results folder.

type: boolean

Options to control the behavior of fastp

fastp option defining the minimum readlength of a read

type: integer

fastp option defining if the reads which failed to be trimmed should be saved

type: boolean

fastp option to define the threshold of quality of an individual base

type: integer

fastp option to define the mean quality for trimming

type: integer
default: 15

fastp option to define if the clipped reads should be saved

type: boolean

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$

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.

required
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.

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

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string
default: GRCh38

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

Path to FASTA genome file.

type: string

This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.

Do not load the iGenomes reference config.

hidden
type: boolean

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

type: boolean
default: true

Directory / URL base for iGenomes references.

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

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.