Introduction Usage Parameters Output

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$

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

Options related to Space Ranger execution and raw spatial data processing

Location of Space Ranger probeset file.

type: string
pattern: ^\S+\.csv$

Location of Space Ranger reference directory. May be packed as tar.gz file.

type: string
default: https://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gz

Additional intermediate output files that can be optionally saved.

Save the extracted tar archive of the Space Ranger reference.

type: boolean

Save extracted tar archives of input data.

type: boolean

Options related to the downstream analyses performed by the pipeline.

Bin size for Visium HD data. Only used for Visium HD. Allowed values: 2, 8, 16.

type: integer

The minimum number of UMIs needed in a spot for that spot to pass the filtering.

type: integer
default: 500

The minimum number of expressed genes in a spot needed for that spot to pass the filtering.

type: integer
default: 250

The minimum number of spots in which a gene is expressed for that gene to pass the filtering.

type: integer
default: 1

The maximum proportion of mitochondrial content that a spot is allowed to have to pass the filtering.

type: number
default: 20

The minimum proportion of ribosomal content that a spot is needs to have to pass the filtering (no filtering is done by default).

type: number

The maximum proportion of haemoglobin content that a spot is allowed to have to pass the filtering (no filtering is done by default).

type: number
default: 100

The number of top highly variable genes to use for the analyses.

type: integer
default: 2000

The resolution for the clustering of the spots.

type: number
default: 1

The method to use for spatially variable gene autocorrelation.

type: string

The number of top spatially variable genes to plot.

type: integer
default: 14

Options related to aggregation of final data objects

Merge per-sample SpatialData objects into one.

type: boolean

Integrate per-sample SpatialData objects into one and output a integration report.

type: boolean

The resolution for the clustering of the spots after integration of samples.

type: number
default: 1

Number of highly variable genes to use for integration of samples.

type: integer
default: 2000

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

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

Display version and exit.

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

Incoming hook URL for messaging service

hidden
type: string

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

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string

Display the help message.

type: boolean,string

Display the full detailed help message.

type: boolean

Display hidden parameters in the help message (only works when —help or —help_full are provided).

type: boolean
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