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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Parameters related to Sopa
Dictionary of parameters to read the raw spatial inputs, e.g., technology name.
objectDictionary of segmentation parameters.
objectDictionary of patches parameters.
objectDictionary of aggregation parameters.
objectDictionary of annotation parameters.
objectDictionary of Xenium Explorer parameters.
objectOptions related to Space Ranger execution and raw spatial data processing
Location of Space Ranger probeset file.
string^\S+\.csv$Location of Space Ranger reference directory. May be packed as tar.gz file.
stringhttps://cf.10xgenomics.com/supp/spatial-exp/refdata-gex-GRCh38-2020-A.tar.gzParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanDo not use coloured log outputs.
booleanIncoming hook URL for messaging service
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