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 4 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

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

If not using the 10X Genomics platform, a custom barcode whitelist can be used with --barcode_whitelist.

type: string

Name of the tool to use for scRNA (pseudo-) alignment.

type: string

The workflow can handle three types of methods:

  • Kallisto/Bustools
  • Salmon Alevin + AlevinQC
  • STARsolo

To choose which one to use, please specify either alevin, star or kallisto as a parameter option for --aligner. By default, the pipeline runs the alevin option. Note that specifying another aligner option also requires choosing appropriate parameters (see below) for the selected option.

The protocol that was used to generate the single cell data, e.g. 10x Genomics v2 Chemistry.

Can be 'auto' (cellranger only), '10XV1', '10XV2', '10XV3', or any other protocol string that will get directly passed the respective aligner.

type: string
default: auto

The default is to auto-detect the protocol when running cellranger. For all other aligners the protocol MUST be manually specified.

The following protocols are recognized by the pipeline and mapped to the corresponding protocol name of the respective aligner: '10XV1', '10XV2', '10XV3'.

Any other protocol value is passed to the aligner in verbatim to support other sequencing platforms. See the kallisto, simpleaf, starsolo, and universc documentations for more details.

This section can be used to disable certain tools in the pipeline

Skip MultiQC Report

type: boolean

Skip FastQC

type: boolean

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

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
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

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.

A cDNA FASTA file

type: string

Reference GTF annotation file

type: string

Specify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.

type: boolean

Directory / URL base for iGenomes references.

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

This can be used to specify a precomputed Salmon index in the pipeline, in order to skip the generation of required indices by Salmon itself.

type: string

Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.

type: string

This is not the same as the kallisto_gene_map parameter down below and is only used by the Salmon Alevin workflow.

It is the target read length the index will be built for, using simpleaf.

type: integer
default: 91

Specify a path to the precomputed STAR index.

type: string

NB: This has to be computed with STAR Version 2.7 or later, as STARsolo was only first supported by STAR Version 2.7.

Ignore the SJDB GTF file.

type: string

Name of sequencing center for BAM read group tag.

type: string

Quantification type of different transcriptomic feature. Use GeneFull on pre-mRNA count for single-nucleus RNA-seq reads. Use Gene Velocyto to generate RNA velocity matrix.

type: string

Params related to Kallisto/BUS tool

Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid --gtf file.

type: string

Specify a path to the precomputed Kallisto index.

type: string

Type of workflow. Use lamanno for RNA velocity based on La Manno et al. 2018 logic. Use nucleus for RNA velocity on single-nucleus RNA-seq reads. Use kite for feature barcoding. Use kite: 10xFB for 10x Genomics Feature Barcoding technology. (default: standard)

type: string

Params related to the Cellranger pipeline

Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.

type: string

Params related to the Cellranger pipeline

Specify a motif file to create a cellranger-arc index. Can be taken, e.g., from the JASPAR database.

type: string

Specify a config file to create the cellranger-arc index.

type: string

Specify the genome reference name used in the config file to create a cellranger-arc index.

type: string

Params related to the Cellranger pipeline

Specify a pre-calculated cellranger index. Readily prepared indexes can be obtained from the 10x Genomics website.

type: string

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.