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

Path to comma-separated file containing information about the Xenium experiment. (eg; meta,path-to-xenium-bundle,path-to-morphology.ome.tif))

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

Mode in which the pipeline is to be run. Either image-based segmentation, coordinate-based segmentation, segmentation-free analysis or data preview.

required
type: string

Segmentation method to run.

type: string

Path to gene panel JSON file to use for relabeling transcripts with the correct gene.

type: string

Polygon segmentation results in GeoJSON format from QuPath.

type: string

Image alignment file containing similarity transform matrix. (e.g., the _imagealignment.csv file exported from Xenium Explorer)

type: string

Model to use for running or starting training.

type: string

Prior segmentation mask from other segmentation methods.

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 for the segmentation layer of the spatialxe pipeline

Whether to run refinement on the image-based segmentation methods. Runs coordinate-based methods after the initial image-based segmentation run.

type: boolean

Whether to relabel genes with gene_panel.json file. True when gene_panel is provided.

type: boolean

Whether to run vanilla xeniumranger workflow.

type: boolean

Whether to only run nucleus segmentation.

type: boolean

Nuclei boundary expansion distance in µm. Default: 5 (Min: 0, Max: 15 if either boundary-stain or interior-stain are enabled and 100 if nucleus-expansion only)

type: integer
default: 5

Minimum intensity in photoelectrons (pe) to filter nuclei. Default: 100. (appropriate range of values is 0 to 99th percentile of image stack or 1000, whichever is larger)

type: integer
default: 100

Specify the name of the interior stain to use or disable. Supported for cell segmentation staining workflow output bundles. Possible options are: “18S” (default) or “disable”

type: boolean
default: true

Specify the name of the boundary stain to use or disable. Supported for cell segmentation staining workflow output bundles. Possible options are: “ATP1A1/CD45/E-Cadherin” (default) or “disable”

type: boolean
default: true

Whether to enhance the morphology.ome.tif file.

type: boolean

Device used for training. (e.g., cuda for GPU or cpu)

type: string

Method for KNN computation. (e.g., cuda for GPU-based computation)

type: string

Preset value for the proseg segmentation method.

type: string
default: xenium

List of image-based segmentation methods.

type: array

List of transcript-based segmentation methods.

type: array

List of segmentation-free methods.

type: array

Regex used to identify or match negative control samples in a dataset.

type: string

List of features to be passed to the ficture method. (eg: TP53,OCIAD1,BCAS3,SOX)

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

Base path / URL for data used in the test profiles.

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

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

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

Do not use coloured log outputs

hidden
type: boolean

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