nf-core/spatialvi
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
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.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringOptions related to Space Ranger execution and raw spatial data processing
Location of Space Ranger probeset file.
string^\S+\.csv$Location of Space Ranger reference directory. May be packed as tar.gz file.
stringhttps://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gzAdditional intermediate output files that can be optionally saved.
Save the extracted tar archive of the Space Ranger reference.
booleanSave extracted tar archives of input data.
booleanOptions related to the downstream analyses performed by the pipeline.
The minimum number of UMIs needed in a spot for that spot to pass the filtering.
integer500The minimum number of expressed genes in a spot needed for that spot to pass the filtering.
integer250The minimum number of spots in which a gene is expressed for that gene to pass the filtering.
integer1The maximum proportion of mitochondrial content that a spot is allowed to have to pass the filtering.
number20The minimum proportion of ribosomal content that a spot is needs to have to pass the filtering (no filtering is done by default).
numberThe maximum proportion of haemoglobin content that a spot is allowed to have to pass the filtering (no filtering is done by default).
number100The number of top highly variable genes to use for the analyses.
integer2000The resolution for the clustering of the spots.
number1The method to use for spatially variable gene autocorrelation.
stringThe number of top spatially variable genes to plot.
integer14Options related to aggregation of final data objects
Merge per-sample SpatialData objects into one.
booleanIntegrate per-sample SpatialData objects into one and output a integration report.
booleanThe resolution for the clustering of the spots after integration of samples.
number1Number of highly variable genes to use for integration of samples.
integer2000Parameters 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/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
stringCustom 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
booleantrueBase 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