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 of all sattelite 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 ./docs/usage.md
Indicates whether input is a tar archive.
booleanSet to true if input is a tar archive. The workflow will extract it then.
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.
Indicates whether dem is a tar archive.
booleanSet to true if dem is a tar archive. The workflow will extract it then.
Water vapor dataset.
stringDirectory containg a number text files describing global water vapor data at different timestamps, and a coordinate order (.coo-)file containig the reference system of the water vapor data.
Indicates whether wvdb is a tar archive.
booleanSet to true if wvdb is a tar archive. The workflow will extract it then.
Datacube definition.
stringA single .prj file describing the projection and reference grid of the generated datacube.
Area of interest.
stringA single vector file specifying the spacial extend of the targeted area.
Endmember definition.
stringA single text file specifying where lines 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 first level data should be processed.
stringLT04,LT05,LE07,S2AString containing comma-separated indicators of satellites in FORCE level 1format. Possible options:
"LT04": Landsat 4 TM,
"LT05": Landsat 5 TM,
"LE07": Landsat 7 ETM+,
"LC08": Landsat 8 OLI,
"S2A": Sentinel-2A MSI,
"S2B": Sentinel-2B MSI
Satellites for which data should be incorporated into higher level processing.
stringLND04 LND05 LND07String 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.
string1984-01-01String with format: "YYYY-MM-DD".
Last day of interest.
string2006-12-31String 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 SWIR2Space-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.
Wheter mosaic visualization should be returned.
booleantrueWhether pyramid visualization should be returned.
booleantrueParameters that configure workflow behavior not directly related to FORCE,
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.
Parameters specific to the FORCE tool.
Number of threads spawned by FORCE for each higher-level or preprocessing task.
integer2Parameters 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.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/