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.
stringSet this to the root directory of all satellite imagery. Directory structure should match format of data downloaded with '$ force-level1-csd ' For concrete directory structure see usage documentation.
Alternatively, a tarball can be supplied. The same directory structure needs to be in place in that tarball.
Digital elevation model.
stringPath to directory containing a subdirectory with tile-wise digital elevation files (.tif) and a virtual dataset file (.vrt file) comprising all tile-wise files from the subdirectory. See usage documentation for details regarding the required structure.
Alternatively, a tarball can be supplied. The same directory structure needs to be in place in that tarball.
Alternatively, a tarball can be supplied. The same directory structure needs to be in place in that tarball.
Water vapor dataset.
stringDirectory containing a number text files describing global water vapor data at different timestamps, and a coordinate order (.coo-)file containing the reference system of the water vapor data. See usage documentation for details regarding the required structure.
Alternatively, a tarball can be supplied. The same directory structure needs to be in place in that tarball.
Datacube definition.
string^\S+\.prj$A single .prj file describing the projection and reference grid of the generated datacube.
Area of interest.
string^\S+\.(gpkg|shp)$A single vector file specifying the spatial extend of the targeted area.
Endmember definition.
string^\S+\.txt$A single text file specifying where rows correspond to satellite bands and columns correspond to endmembers. Values correspond to reflectance values and are separated by spaces.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
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|$))+$String containing space-separated indicators of satellites in FORCE level 2 format. Common options: "LND04": 6-band Landsat 4 TM, "LND05": 6-band Landsat 5 TM, "LND07": 6-band Landsat 7 ETM+, "LND08/09": 6-band Landsat 8-9 OLI, "SEN2A": 10-band Sentinel-2A, "SEN2B": 10-band Sentinel-2B, all options here
First day of interest.
string1984-01-01^\d{4}-\d{2}-\d{2}$String with format: "YYYY-MM-DD".
Last day of interest.
string2006-12-31^\d{4}-\d{2}-\d{2}$String with format: "YYYY-MM-DD".
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|$))+Space-separated list of indexes and bands that should be considered in time series analyses. They are indicated by using their established abbreviations. The full list of available indexes is available at https://force-eo.readthedocs.io/en/latest/components/higher-level/tsa/param.html under the 'INDEX' parameter. Spectral unmixing is a special index and always activated.
Should the full time series stack be returned.
booleanThis parameter enables or disables the output of the time series stack for each tile and band/index. Here, each band shows the values of a single date.
Enable 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.
booleanBy default, the results of preprocessing (aka. analyses ready data or level-2 data) are not published. Setting this parameter to true enforces that these files are published to the output directory.
Whether the results of time series analyses should be published to the output directory.
booleanBy default, the results of higher level processing (aka. level-3 data) are not published. Setting this parameter to true enforces that these files are published to the output directory.
Batch size of tiles considered for merging.
integer100Controls trade-off between parallelism and I/O load. Higher group_size -> More tiles merged in one process, less I/O load. Lower group_size -> Less tiles merged in one process, more I/O load.
Publish pipeline outputs.
booleantrueSet to false to prevent all modules from publishing their results.
Parameters 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/masterIf you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.
Institutional 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.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
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
stringIncoming hook URL for messaging service. Currently, MS Teams and Slack are supported.
Custom 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