nf-core/rangeland
Pipeline for remotely sensed imagery. The pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes.
Define where the pipeline should find input data and save output data.
Root directory or tarball of all satellite imagery.
stringDigital elevation model.
stringWater vapor dataset.
stringDatacube definition.
string^\S+\.prj$Area of interest.
string^\S+\.(gpkg|shp)$Endmember definition.
string^\S+\.txt$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringDefinition of satellite image parameters.
Satellites for which data should be incorporated into higher level processing.
stringLND04 LND05 LND07^((LND04|LND05|LND07|LND08|LND09|SEN2A|SEN2B|sen2a|sen2b|S1AIA|S1BIA|S1AID|S1BID|MOD01|MOD02|LNDLG|SEN2L|SEN2H|R-G-B|VVVHP|MODIS)(\s|$))+$First day of interest.
string1984-01-01^\d{4}-\d{2}-\d{2}$Last day of interest.
string2006-12-31^\d{4}-\d{2}-\d{2}$Spatial resolution applied in analyses.
integer30Modify higher level processing behaviour.
Select which bands and indexes should be considered in time series analyses.
stringNDVI BLUE GREEN RED NIR SWIR1 SWIR2((BLUE|GREEN|RED|NIR|SWIR1|SWIR2|RE1|RE2|RE3|BNIR|NDVI|EVI|NBR|NDTI|ARVI|SAVI|SARVI|TC-BRIGHT|TC-GREEN|TC-WET|TC-DI|NDBI|NDWI|MNDWI|NDMI|NDSI|SMA|kNDVI|NDRE1|NDRE2|CIre|NDVIre1|NDVIre2|NDVIre3|NDVIre1n|NDVIre2n|NDVIre3n|MSRre|MSRren,CCI)(\s|$))+Should the full time series stack be returned.
booleanEnable or disable visualizations.
Whether mosaic visualization should be returned.
booleantrueWhether pyramid visualization should be returned.
booleantrueParameters that configure workflow behavior not directly related to FORCE,
Whether analysis ready data should be published to the output directory.
booleanWhether the results of time series analyses should be published to the output directory.
booleanBatch size of tiles considered for merging.
integer100Publish pipeline outputs.
booleantrueParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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