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.
string
Email 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.
string
Options 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.
string
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.
boolean
Save extracted tar archives of input data.
boolean
Options 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.
integer
500
The minimum number of expressed genes in a spot needed for that spot to pass the filtering.
integer
250
The minimum number of spots in which a gene is expressed for that gene to pass the filtering.
integer
1
The maximum proportion of mitochondrial content that a spot is allowed to have to pass the filtering.
number
20
The minimum proportion of ribosomal content that a spot is needs to have to pass the filtering (no filtering is done by default).
number
The maximum proportion of haemoglobin content that a spot is allowed to have to pass the filtering (no filtering is done by default).
number
100
The number of top highly variable genes to use for the analyses.
integer
2000
The resolution for the clustering of the spots.
number
1
The method to use for spatially variable gene autocorrelation.
string
The number of top spatially variable genes to plot.
integer
14
Options related to aggregation of final data objects
Merge per-sample SpatialData objects into one.
boolean
Integrate per-sample SpatialData objects into one and output a integration report.
boolean
The resolution for the clustering of the spots after integration of samples.
number
1
Number of highly variable genes to use for integration of samples.
integer
2000
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
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.
string