nf-core/sopa
Nextflow version of Sopa - spatial omics pipeline and analysis
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})$
Parameters related to Sopa
Dictionary of parameters to read the raw spatial inputs, e.g., technology name.
object
Dictionary of segmentation parameters.
object
Dictionary of patches parameters.
object
Dictionary of aggregation parameters.
object
Dictionary of annotation parameters.
object
Dictionary of Xenium Explorer parameters.
object
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
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
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
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