nf-core/spatialxe
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))
string^\S+\.csv$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringMode in which the pipeline is to be run. Either image-based or coordinate-based approach.
stringSegmentation method to run.
stringPath to gene panel JSON file to use for relabeling transcripts with the correct gene.
stringPolygon segmentation results in GeoJSON format from QuPath.
stringImage alignment file containing similarity transform matrix. (e.g., the _imagealignment.csv file exported from Xenium Explorer)
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringOptions for the segmentation layer of the spatialxe pipeline
Whether to generate a preview of the dataset with the transcripts.csv.gz.
booleanWhether to run refinement on the image-based segmentation methods. Runs coordinate-based methods after the initial image-based segmentation run.
booleanWhether to relabel genes with gene_panel.json file. True when gene_panel is provided.
booleanWhether to run vanilla xeniumranger workflow.
booleanWhether to only run nucleus segmentation.
booleanNuclei 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)
integer5Minimum 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)
integer100Specify 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"
booleantrueSpecify 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"
booleantrueWhether to enhance the morphology.ome.tif file.
booleanDevice used for training. (e.g., cuda for GPU or cpu)
stringMethod for KNN computation. (e.g., cuda for GPU-based computation)
stringModel to use for running or starting training. (eg. cyto3 or nuclei)
stringPreset value for the proseg segmentation method.
stringxeniumList of image-based segmentation methods.
arrayList of transcript-based segmentation methods.
arrayList of segmentation-free methods.
arrayRegex used to identify or match negative control samples in a dataset.
stringList of features to be passed to the ficture method. (eg: TP53,OCIAD1,BCAS3,SOX)
stringWhether to run bayor with image/segmentation-mask.
booleantrueWhether to run baysor with transcripts.csv.gz.
booleanWhether to create a preview of the dataset with transcripts.csv.gz.
booleanParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf 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.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringBase path / URL for data used in the test profiles.
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/spatialxeLess common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringCustom MultiQC yaml file containing HTML including a methods description.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueDo not use coloured log outputs
booleanBase URL or local path to location of pipeline test dataset files
stringhttps://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
string