nf-core · Felix-Kummer · Jun 2, 2025 · Apr 21, 2025 · May 18, 2025 · May 19, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,24 +3,35 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0.0 - [2025-01-17]
-
-First release of `nf-core/rangeland`.
-This work is a continuation, and nf-core port, of the [original version of this pipeline](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland).
+# v1.1.0dev - [date]
 
 ### `Added`
 
+- [26](https://github.com/nf-core/rangeland/pull/26) Meta maps
+- [26](https://github.com/nf-core/rangeland/pull/26) Parameterization for preprocessing and higher-level processing
+
+### `Changed`
+
+- [24](https://github.com/nf-core/rangeland/pull/24) Update to FORCE version 3.8.01
+- [25](https://github.com/nf-core/rangeland/pull/25) Template update for nf-core/tools v3.2.1
+- [26](https://github.com/nf-core/rangeland/pull/26) Preparation for FORCE nf-core modules
+
 ### `Fixed`
 
 ### `Dependencies`
 
 ### `Deprecated`
 
-## v1.1.0dev - [date]
+- [26](https://github.com/nf-core/rangeland/pull/26) Parameter file processes
+
+## v1.0.0 - [2025-01-17]
+
+First release of `nf-core/rangeland`.
+This work is a continuation, and nf-core port, of the [original version of this pipeline](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland).
 
 ### `Added`
 
-- [24](https://github.com/nf-core/rangeland/pull/24) Update to FORCE version 3.8.01
+### `Changed`
 
 ### `Fixed`
 

diff --git a/README.md b/README.md
@@ -19,17 +19,16 @@
 
 ## Introduction
 
-**nf-core/rangeland** is a geographical best-practice analysis pipeline for remotely sensed imagery.
+**nf-core/rangeland** is a best-practice Earth Observation analysis 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. The main pipeline steps are:
 
-1. Read satellite imagery, digital elevation model (dem), endmember definition, water vapor database (wvdb), datacube definition and area of interest definition (aoi)
+1. Read satellite imagery, datacube definition, area of interest definition (aoi) and optional inputs such as digital elevation model (dem), endmember definition and water vapor database (wvdb)
 2. Generate allow list and analysis mask to determine which pixels from the satellite data can be used
 3. Preprocess data to obtain atmospherically corrected images alongside quality assurance information (aka. level 2 analysis read data)
-4. Merge spatially and temporally overlapping preprocessed data
-5. Classify pixels by applying linear spectral unmixing
-6. Time series analyses to obtain trends in vegetation dynamics to derive level 3 data
-7. Create mosaic and pyramid visualizations of the results
-8. Version reporting with MultiQC ([`MultiQC`](http://multiqc.info/))
+4. Merge preprocessed data based on spatially and temporally overlap
+5. Time series analyses to obtain trends in vegetation dynamics to derive level 3 data
+6. Create mosaic and pyramid visualizations of the results
+7. Version reporting with MultiQC ([`MultiQC`](http://multiqc.info/))
 
 <p align="center">
     <img title="nf-core/rangeland diagram" src="docs/images/rangeland_diagram.png" width=95%>
@@ -40,23 +39,37 @@ The pipeline processes satellite imagery alongside auxiliary data in multiple st
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-To run, satellite imagery, water vapor data, a digital elevation model, endmember definitions, a datacube specification, and a area-of-interest specification are required as input data.
+To run, satellite imagery, datacube specification, and a area-of-interest specification are required as input.
+It is highly recommended to also provide data water vapor data, a digital elevation model and a endmember definition.
 Please refer to the [usage documentation](https://nf-co.re/rangeland/usage) for details on the input structure.
 
 Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/rangeland \
-   -profile <docker/singularity/.../institute> \
-   --input <SATELLITE IMAGES> \
-   --dem <DIGITAL ELEVATION MODEL> \
-   --wvdb <WATER VAPOR DATA> \
-   --data_cube <DATA CUBE> \
-   --aoi <AREA OF INTEREST> \
-   --endmember <ENDMEMBER SPECIFICATION> \
-   --outdir <OUTDIR>
+    -profile <docker/singularity/.../institute> \
+    --input <SATELLITE IMAGES> \
+    --data_cube <DATA CUBE> \
+    --aoi <AREA OF INTEREST> \
+    --outdir <OUTDIR>
 ```
 
+The following parameters should be added for optimal results:
+
+```bash
+    --dem <DIGITAL ELEVATION MODEL> \
+    --wvdb <WATER VAPOR DATA> \
+    --endmember <ENDMEMBER SPECIFICATION>
+```
+
+To enable spectral unmixing, and use the endmember file, the `--indexes` parameters should contain `SMA`, e.g.:
+
+```bash
+    --indexes "SMA NDVI BLUE GREEN RED NIR SWIR1 SWIR2"
+```
+
+See the [usage documentation](./docs/usage.md#higher-level-processing-indexes) for more details on indexes.
+
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
@@ -83,7 +96,7 @@ nf-core alignment started on the [nf-core branch of the original repository](htt
 We thank the following people for their extensive assistance in the development of this pipeline:
 
 - [Fabian Lehmann](https://github.com/Lehmann-Fabian)
-- [Katarzyna Ewa Lewinska](https://github.com/kelewinska).
+- [Katarzyna Ewa Lewinska](https://github.com/kelewinska)
 
 ## Acknowledgements
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -38,7 +38,7 @@ process {
     }
 
     withName: "FORCE_PREPROCESS" {
-        publishDir    = [
+        publishDir = [
             [
                 path:    { "${params.outdir}/preprocess/${task.tag}/logs" },
                 mode:    params.publish_dir_mode,
@@ -51,35 +51,40 @@ process {
                 pattern: 'level2_ard/**/*',
                 saveAs:  { params.save_ard ? it : null },
                 enabled: params.publish_dir_enabled
+            ],
+            [
+                path:    { "${params.outdir}/preprocess/${task.tag}/param_files" },
+                mode:    params.publish_dir_mode,
+                pattern: '*.prm',
+                enabled: params.publish_dir_enabled
             ]
         ]
     }
 
-
-    withName: "HIGHER_LEVEL_CONFIG" {
-        publishDir    = [
-            path:    { "${params.outdir}/higher-level/${task.tag}/param_files" },
-            mode:    params.publish_dir_mode,
-            pattern: '*.prm',
-            enabled: params.publish_dir_enabled
-        ]
-    }
-
     withName: "FORCE_HIGHER_LEVEL" {
         publishDir = [
-            path:    { "${params.outdir}/higher-level/${task.tag}" },
-            mode:    params.publish_dir_mode,
-            pattern: 'trend/*.tif',
-            saveAs:  { params.save_ard ? "trend_files/${it.tokenize('/')[-1]}" : null },
-            enabled: params.publish_dir_enabled
+            [
+                path:    { "${params.outdir}/higher-level/${task.tag}" },
+                mode:    params.publish_dir_mode,
+                pattern: 'trend/*.tif',
+                saveAs:  { params.save_tsa ? "trend_files/${it.tokenize('/')[-1]}" : null },
+                enabled: params.publish_dir_enabled
+            ],
+            [
+                path:    { "${params.outdir}/higher-level/${task.tag}/param_files" },
+                mode:    params.publish_dir_mode,
+                pattern: '*.prm',
+                enabled: params.publish_dir_enabled
+            ]
+
         ]
     }
 
     withName: "FORCE_PYRAMID" {
         stageInMode = 'copy'
         publishDir  = [
             path:    { "${params.outdir}/trend/pyramid/" },
-            saveAs:  { "${it.substring(12,it.indexOf("."))}/trend/${it.substring(0,11)}/$it" },
+            saveAs:  { "${meta.product}/trend/${task.tag}/$it" },
             pattern: '*.tif*',
             mode:    params.publish_dir_mode,
             enabled: params.publish_dir_enabled
@@ -107,15 +112,6 @@ process {
         ]
     }
 
-    withName: "PREPROCESS_CONFIG" {
-        publishDir    = [
-            path:    { "${params.outdir}/preprocess/${task.tag}/param_files" },
-            mode:    params.publish_dir_mode,
-            pattern: '*.prm',
-            enabled: params.publish_dir_enabled
-        ]
-    }
-
     withName: 'MULTIQC' {
         ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
         publishDir = [

diff --git a/conf/test.config b/conf/test.config
@@ -42,10 +42,31 @@ params {
 
     // enable mosaic visualization
     mosaic_visualization  = true
+
+    // indexes for higher-level processing
+    indexes = "SMA NDVI BLUE GREEN RED NIR SWIR1 SWIR2"
+
 }
 
 process {
     withName: "UNTAR_*" {
         ext.args2   = "--strip-components=0"
     }
+
+    // Disable OVV preprocessing output
+    withName: "FORCE_PREPROCESS" {
+        ext.args = { [ "OUTPUT_OVV":"FALSE" ] }
+    }
+
+    // Enable RBF interpolation, define required polarmetrics (and their outputs)
+    withName: "FORCE_HIGHER_LEVEL" {
+        ext.args = { [
+                        "INTERPOLATE": "RBF",
+                        "INT_DAY"    : 16,
+                        "POL"        : "VPS VBL VSA",
+                        "OUTPUT_POL" : "TRUE",
+                        "OUTPUT_TRO" : "TRUE",
+                        "OUTPUT_CAO" : "TRUE"
+                    ] }
+    }
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -28,18 +28,41 @@ params {
     start_date = '1986-01-01'
     end_date   = '1989-12-31'
 
+    // sensor level for higher-level processing
     sensors_level2 = 'LND04 LND05'
 
-    // Enable time series stack output
-    return_tss = true
-
     // Enable mosaic visualization
     mosaic_visualization  = true
+
+    // Enable higher-level publishing
+    save_tsa = true
+
+    // indexes for higher-level processing
+    indexes = "SMA NDVI BLUE GREEN RED NIR SWIR1 SWIR2"
+
 }
 
 process {
     // This is required because of the internal structure of the input tarballs
     withName: "UNTAR_*" {
-        ext.args2   = "--strip-components=1"
+        ext.args2 = "--strip-components=1"
+    }
+
+    // Enable time series stack output, enable RBF interpolation, define required polarmetrics (and their outputs)
+    withName: "FORCE_HIGHER_LEVEL" {
+        ext.args  = { [
+                        "OUTPUT_TSS" : "TRUE",
+                        "INTERPOLATE": "RBF",
+                        "INT_DAY"    : 16,
+                        "POL"        : "VPS VBL VSA",
+                        "OUTPUT_POL" : "TRUE",
+                        "OUTPUT_TRO" : "TRUE",
+                        "OUTPUT_CAO" : "TRUE"
+                    ] }
+    }
+
+    // Disable OVV preprocessing output
+    withName: "FORCE_PREPROCESS" {
+        ext.args = { [ "OUTPUT_OVV":"FALSE" ] }
     }
 }
diff --git a/docs/images/rangeland_diagram.png b/docs/images/rangeland_diagram.png
diff --git a/docs/images/rangeland_diagram.svg b/docs/images/rangeland_diagram.svg