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

Input FastQ files

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})$

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 protocol that was used to generate the single cell data, e.g. 10XV2 (default).

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

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

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

A cDNA FASTQ file

type: string

Reference GTF annotation file

type: string

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

type: string

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

Specify a path to the precomputed STAR index.

type: string

Ignore the SJDB GTF file.

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

If set to false, skip the correct steps after mapping with Kallisto.

type: boolean

Skip BUStools entirely in workflow

type: boolean

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

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|day)\s*)+$

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

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

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

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

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean

Skip the MultiQC reporting feature in the pipeline.

type: boolean