nf-core · Felix-Kummer · Mar 24, 2026 · Mar 17, 2026 · Mar 17, 2026 · Mar 20, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [32](https://github.com/nf-core/rangeland/pull/32) Template update for nf-core/tools v3.5.1
 - [33](https://github.com/nf-core/rangeland/pull/33) Nextflow strict syntax update
 - [34](https://github.com/nf-core/rangeland/pull/34) Update nf-core subworkflows
+- [39](https://github.com/nf-core/rangeland/pull/39) Update to FORCE version v3.10.04
 
 ### `Fixed`
 

diff --git a/bin/test.R b/bin/test.R
@@ -9,13 +9,13 @@ args = commandArgs(trailingOnly=TRUE)
 
 
 if (length(args) != 7 && length(args) != 2) {
-    stop("\n Error: wrong number of parameters. Usage: \n 1st arg: workflow results directory (mosaic)
+    stop("\n Error: wrong number of parameters. Usage: \n 1st arg: staged workflow results directory
         \n 2nd-7th args:  reference rasters (*.tif) in order:
         woody cover change, woody cover year of change,
         herbaceous cover change, herbaceous cover year of change,
         peak change, peak year of change
         \nor \n
-        1st arg: workflow results directory (mosaic) \n 2nd arg: reference directory
+        1st arg: staged workflow results directory \n 2nd arg: reference directory
         ", call.=FALSE)
 }
 
@@ -48,6 +48,50 @@ compare_direction <- function(r1, r2, threshold = 0.95) {
     }
 }
 
+# function to load staged pipeline outputs without relying on upstream VRT paths
+load_product_rast <- function(root_dir, product_suffix) {
+    tif_files <- sort(list.files(
+        root_dir,
+        pattern = paste0(product_suffix, "\\.tif$"),
+        recursive = TRUE,
+        full.names = TRUE
+    ))
+
+    if (length(tif_files) == 0) {
+        stop(
+            paste0(
+                "No staged TIFFs found for product '",
+                product_suffix,
+                "' under ",
+                root_dir
+            ),
+            call. = FALSE
+        )
+    }
+
+    if (length(tif_files) == 1) {
+        return(rast(tif_files))
+    }
+
+    merge(sprc(lapply(tif_files, rast)))
+}
+
+get_change_band <- function(r) {
+    if ("CHANGE" %in% names(r)) {
+        return(r$CHANGE)
+    }
+
+    r[[1]]
+}
+
+get_yoc_band <- function(r) {
+    if ("YEAR-OF-CHANGE" %in% names(r)) {
+        return(r["YEAR-OF-CHANGE"])
+    }
+
+    r[[3]]
+}
+
 
 # LOAD REFERENCE
 #######################################################################
@@ -87,37 +131,31 @@ if (length(args) == 7 ){
 # input data dir
 dinp <- args[1]
 
-fname <- dir(dinp, ".*HL_TSA_LNDLG_SMA_VBL-CAO.vrt$", full.names=TRUE)
-
-woody_cover_rast <- rast(fname)
+woody_cover_rast <- load_product_rast(dinp, "HL_TSA_LNDLG_SMA_VBL-CAO")
 
-woody_cover_changes        <- woody_cover_rast$CHANGE
-woody_cover_year_of_change <- woody_cover_rast["YEAR-OF-CHANGE"]
+woody_cover_changes        <- get_change_band(woody_cover_rast)
+woody_cover_year_of_change <- get_yoc_band(woody_cover_rast)
 
 
 
 # HERBACEOUS COVER CHANGE (VALUE OF SEASONAL APLITUDE)
 #######################################################################
 
 
-fname <- dir(dinp, ".*HL_TSA_LNDLG_SMA_VSA-CAO.vrt$", full.names=TRUE)
+herbaceous_cover_rast <- load_product_rast(dinp, "HL_TSA_LNDLG_SMA_VSA-CAO")
 
-herbaceous_cover_rast <- rast(fname)
-
-herbaceous_cover_changes        <- herbaceous_cover_rast$CHANGE
-herbaceous_cover_year_of_change <- herbaceous_cover_rast["YEAR-OF-CHANGE"]
+herbaceous_cover_changes        <- get_change_band(herbaceous_cover_rast)
+herbaceous_cover_year_of_change <- get_yoc_band(herbaceous_cover_rast)
 
 
 
 # VALUE OF PEAK SEASON
 #######################################################################
 
-fname <- dir(dinp, ".*HL_TSA_LNDLG_SMA_VPS-CAO.vrt$", full.names=TRUE)
-
-peak_rast <- rast(fname)
+peak_rast <- load_product_rast(dinp, "HL_TSA_LNDLG_SMA_VPS-CAO")
 
-peak_changes        <- peak_rast$CHANGE
-peak_year_of_change <- peak_rast["YEAR-OF-CHANGE"]
+peak_changes        <- get_change_band(peak_rast)
+peak_year_of_change <- get_yoc_band(peak_rast)
 
 
 

diff --git a/docs/output.md b/docs/output.md
@@ -158,9 +158,10 @@ The `.tif` files are only published when the `--save_tsa` parameter is set to `t
 <summary>Output files</summary>
 
 - `trend/`
-  - `mosaic/<PRODUCT>/`
-    - `<TILE>/`: .tif files that are part of the mosaic.
-    - `mosaic/`: Contains a single virtual raster file that combines the .tif files into the mosaic visualization.
+  - `mosaic/`
+    - `<PRODUCT>/`: Contains all files for a single product mosaic.
+      - `<PRODUCT>.vrt` Virtual raster file for the product. This can be opened in GIS systems to view the mosaic for the product.
+      - `<TILE>`: Contains the tile data used in `.vrt` file for this mosaic.
   - `pyramid/<TREND_TYPE>/trend/<TILE>/`: Contains tile-wise pyramid visualizations for every trend analyzed in the workflow.
 
 </details>

diff --git a/docs/usage.md b/docs/usage.md
@@ -471,24 +471,40 @@ process {
 
 For a comprehensive list of parameters see the FORCE documentation on [force-l2ps parameterization](https://force-eo.readthedocs.io/en/latest/components/lower-level/level2/param.html#l2-param) and [force-higher-level (TSA) parameterization](https://force-eo.readthedocs.io/en/latest/components/higher-level/tsa/param.html).
 
+#### Preprocessing (FORCE_PREPROCESS)
+
 The following FORCE parameters can _not_ be set through `task.ext.args` in preprocessing (for the `FORCE_PREPROCESS` process):
 
 - `FILE_QUEUE`: This pipeline processes one image per process, which does not require a queue for input files.
 - `DIR_LEVEL2`, `DIR_LOG`, `DIR_PROVENANCE`, `DIR_TEMP`: FORCE directories must be defined within the process working directory.
 - `FILE_DEM`: Set through process's input channels and derived from `params.dem`, see [digital elevation model](#digital-elevation-model-dem) for details.
+- `USE_DEM_DATABASE`: Not implemented yet.
 - `FILE_TILE`: Set through the process's input channels.
 - `TILE_SIZE`: Derived from datacube input channel, which is created based on the [datacube input](#datacube).
-- `BLOCK_SIZE`: Derived from datacube input channel, which is created based on the [datacube input](#datacube)..
-- `ORIGIN_LON`: Derived from datacube input channel, which is created based on the [datacube input](#datacube)..
-- `ORIGIN_LAT`: Derived from datacube input channel, which is created based on the [datacube input](#datacube)..
-- `PROJECTION`: Derived from datacube input channel, which is created based on the [datacube input](#datacube)..
+- `ORIGIN_LON`: Derived from datacube input channel, which is created based on the [datacube input](#datacube).
+- `ORIGIN_LAT`: Derived from datacube input channel, which is created based on the [datacube input](#datacube).
+- `PROJECTION`: Derived from datacube input channel, which is created based on the [datacube input](#datacube).
 - `WVP`: Set through process's input channels and derived from `--wvdb`, see [water vapor database](#water-vapor-database-wvdb) for details.
 - `DIR_AOD`: Set through process's input channels and derived from `--aod`, see [aerosol optical depth](#aerosol-optical-depth-aod) for details.
 - `DIR_COREG_BASE`: Set through process's input channels and derived from `--coreg`, see [coregistration](#coregistration-near-infrared-nir-data) for details.
 - `FILE_AOI`: Set through process's input channels and derived from `--aoi`, see [area of interest](#area-of-interest-aoi) for details.
 
+The following parameter's default values deviate from their current FORCE default:
+
+- `OUTPUT_FORMAT`: set to `GTiff`(GeoTIFF) instead of `COG` (cloud optimized GeoTIFF)
+
 In addition, the `DO_TOPO` FORCE parameter will only be considered when the [pipeline is executed with a digital elevation model](#digital-elevation-model-dem).
 
+> [!WARNING]
+> Please refer to the FORCE documentation as mentioned above to understand the impact of different parameters.
+> Certain combinations of parameters may break FORCE or the pipeline.
+>
+> The `OUTPUT_FORMAT` parameters and `FILE_OUTPUT_OPTIONS` should be modified with caution.
+> The pipeline expects both modules to return `.tif` files. Other output formats will break the pipeline.
+> In addition, certain combinations of these parameters may require custom containers (e.g. container with COG GDAL drivers for `OUTPUT_FORMAT` = `COG`.)
+
+#### Higher-level processing (FORCE_HIGHER_LEVEL)
+
 The following FORCE parameters can _not_ be set through `task.ext.args` in higher-level processing (for the `FORCE_HIGHER_LEVEL` process):
 
 - `DIR_LOWER`, `DIR_HIGHER`, `DIR_PROVENANCE`: FORCE directories must be defined within the process working directory.

diff --git a/modules/local/check_results/main.nf b/modules/local/check_results/main.nf
@@ -21,13 +21,8 @@ process CHECK_RESULTS {
 
     script:
     """
-    files=`find ./trend/ -maxdepth 1 -mindepth 1 -type d`
-    for path in \$files; do
-        mkdir -p trend/\$(ls \$path)
-        cp \$path/*/* trend/\$(ls \$path)/
-        rm \$path -r
-    done;
-    test.R trend/mosaic $woody_change_ref $woody_yoc_ref $herbaceous_change_ref $herbaceous_yoc_ref $peak_change_ref $peak_yoc_ref
+    # run check results
+    test.R ./trend $woody_change_ref $woody_yoc_ref $herbaceous_change_ref $herbaceous_yoc_ref $peak_change_ref $peak_yoc_ref
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/check_results_full/main.nf b/modules/local/check_results_full/main.nf
@@ -16,13 +16,7 @@ process CHECK_RESULTS_FULL {
 
     script:
     """
-    files=`find ./trend/ -maxdepth 1 -mindepth 1 -type d`
-    for path in \$files; do
-        mkdir -p trend/\$(ls \$path)
-        cp \$path/*/* trend/\$(ls \$path)/
-        rm \$path -r
-    done;
-    test.R trend/mosaic $reference
+    test.R ./trend $reference
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/force-generate_analysis_mask/main.nf b/modules/local/force-generate_analysis_mask/main.nf
@@ -2,7 +2,7 @@ process FORCE_GENERATE_ANALYSIS_MASK{
     tag { aoi.simpleName }
     label 'process_single'
 
-    container "nf-core/force:3.8.01"
+    container "nf-core/force:3.10.04"
 
     input:
     path aoi

diff --git a/modules/local/force-generate_tile_allow_list/main.nf b/modules/local/force-generate_tile_allow_list/main.nf
@@ -2,7 +2,7 @@ process FORCE_GENERATE_TILE_ALLOW_LIST{
     tag { aoi.simpleName }
     label 'process_single'
 
-    container "nf-core/force:3.8.01"
+    container "nf-core/force:3.10.04"
 
     input:
     path aoi

diff --git a/modules/local/force-higher_level/main.nf b/modules/local/force-higher_level/main.nf
@@ -3,11 +3,11 @@ process FORCE_HIGHER_LEVEL {
     label 'process_medium'
     label 'error_retry'
 
-    container "nf-core/force:3.8.01"
+    container "nf-core/force:3.10.04"
 
     input:
     tuple val(meta), path(boa), path(qai), path(mask)
-    path 'ard/datacube-definition.prj'
+    path cube
     path endmember
     path allow_list
     val resolution
@@ -53,6 +53,7 @@ process FORCE_HIGHER_LEVEL {
     def outputOptions      = task.ext.args?.getAt("FILE_OUTPUT_OPTIONS")   ? "FILE_OUTPUT_OPTIONS = ${task.ext.args["FILE_OUTPUT_OPTIONS"]}"     : "FILE_OUTPUT_OPTIONS = NULL"
     def outputExplode      = task.ext.args?.getAt("OUTPUT_EXPLODE")        ? "OUTPUT_EXPLODE = ${task.ext.args["OUTPUT_EXPLODE"]}"               : "OUTPUT_EXPLODE = FALSE"
     def outputSubDirs      = "OUTPUT_SUBFOLDERS = FALSE"
+    def failIfEmpty        = task.ext.args?.getAt("FAIL_IF_EMPTY")         ? "FAIL_IF_EMPTY = ${task.ext.args["FAIL_IF_EMPTY"]}"                 : "FAIL_IF_EMPTY = FALSE"
 
     // Parallel processing
     def nThreadRead        = task.ext.args?.getAt("NTHREAD_READ")          ? "NTHREAD_READ = ${task.ext.args["NTHREAD_READ"]}"                   : "NTHREAD_READ = 8"
@@ -65,13 +66,14 @@ process FORCE_HIGHER_LEVEL {
     def xTilePrm           = "X_TILE_RANGE = $xTile $xTile"
     def yTilePrm           = "Y_TILE_RANGE = $yTile $yTile"
     def fileTile           = allow_list                                    ? "FILE_TILE = $allow_list"                                           : "FILE_TILE = NULL"
-    def blockSize          = task.ext.args?.getAt("BLOCK_SIZE")            ? "BLOCK_SIZE = ${task.ext.args["BLOCK_SIZE"]}"                       : "BLOCK_SIZE = 0"
+    def chunkSize          = task.ext.args?.getAt("CHUNK_SIZE")            ? "CHUNK_SIZE = ${task.ext.args["CHUNK_SIZE"]}"                       : "CHUNK_SIZE = 0 0"
     def res                = "RESOLUTION = $resolution"
     def reducePSF          = task.ext.args?.getAt("REDUCE_PSF")            ? "REDUCE_PSF = ${task.ext.args["REDUCE_PSF"]}"                       : "REDUCE_PSF = FALSE"
     def useL2Improph       = task.ext.args?.getAt("USE_L2_IMPROPHE")       ? "USE_L2_IMPROPHE = ${task.ext.args["USE_L2_IMPROPHE"]}"             : "USE_L2_IMPROPHE = FALSE"
 
     // Sensor allow list
     def sensors            = "SENSORS $sensors_level2"
+    def targetSensor       = task.ext.args?.getAt("TARGET_SENSOR")         ? "TARGET_SENSOR = ${task.ext.args["TARGET_SENSOR"]}"                 : "TARGET_SENSOR = LNDLG"
     def productTypeMain    = task.ext.args?.getAt("PRODUCT_TYPE_MAIN")     ? "PRODUCT_TYPE_MAIN = ${task.ext.args["PRODUCT_TYPE_MAIN"]}"         : "PRODUCT_TYPE_MAIN = BOA"
     def productTypeQuality = task.ext.args?.getAt("PRODUCT_TYPE_QUALITY")  ? "PRODUCT_TYPE_QUALITY = ${task.ext.args["PRODUCT_TYPE_QUALITY"]}"   : "PRODUCT_TYPE_QUALITY = QAI"
     def spectralAdjust     = task.ext.args?.getAt("SPECTRAL_ADJUST")       ? "SPECTRAL_ADJUST = ${task.ext.args["SPECTRAL_ADJUST"]}"             : "SPECTRAL_ADJUST = FALSE"
@@ -170,7 +172,16 @@ process FORCE_HIGHER_LEVEL {
     mkdir -p $ardPath
     mv *.tif $ardPath
 
+
+    # set chunk size
+    CHUNKSIZE='${chunkSize}'
+    if [[ "\$CHUNKSIZE" == "CHUNK_SIZE = 0 0" ]]; then
+        TILESIZE=\$(sed '6q;d' $cube)
+        CHUNKSIZE="CHUNK_SIZE = \$TILESIZE"
+    fi
+
     # create parameter file
+    mv "$cube" "${ardBasePath}datacube-definition.prj"
 
     PARAM=./tsa_${meta.id}.prm
     cat <<EOF > \$PARAM
@@ -184,6 +195,7 @@ process FORCE_HIGHER_LEVEL {
     ${outputOptions}
     ${outputExplode}
     ${outputSubDirs}
+    ${failIfEmpty}
     ${nThreadRead}
     ${nThreadCompute}
     ${nThreadWrite}
@@ -192,11 +204,12 @@ process FORCE_HIGHER_LEVEL {
     ${xTilePrm}
     ${yTilePrm}
     ${fileTile}
-    ${blockSize}
+    \$CHUNKSIZE
     ${res}
     ${reducePSF}
     ${useL2Improph}
     ${sensors}
+    ${targetSensor}
     ${productTypeMain}
     ${productTypeQuality}
     ${spectralAdjust}

diff --git a/modules/local/force-mosaic/main.nf b/modules/local/force-mosaic/main.nf
@@ -2,7 +2,7 @@ process FORCE_MOSAIC{
     tag { meta.id }
     label 'process_low'
 
-    container "nf-core/force:3.8.01"
+    container "nf-core/force:3.10.04"
 
     input:
     tuple val(meta), path('trend/*')

diff --git a/modules/local/force-preprocess/main.nf b/modules/local/force-preprocess/main.nf
@@ -3,7 +3,7 @@ process FORCE_PREPROCESS {
     label 'process_medium'
     label 'error_retry'
 
-    container "nf-core/force:3.8.01"
+    container "nf-core/force:3.10.04"
 
     input:
     tuple val(meta), path(data)
@@ -53,14 +53,15 @@ process FORCE_PREPROCESS {
 
     // Digital elevation model
     // "FILE_DEM"     can only be set after input stage-in
+    def useDemDB      = "USE_DEM_DATABASE = FALSE"
+    def demResampling = task.ext.args?.getAt("DEM_RESAMPLING")         ? "DEM_RESAMPLING = ${task.ext.args["DEM_RESAMPLING"]}"               : "DEM_RESAMPLING = BL"
     def demNoData     = task.ext.args?.getAt("DEM_NODATA")             ? "DEM_NODATA = ${task.ext.args["DEM_NODATA"]}"                       : "DEM_NODATA = -32767"
 
     // Data cubes
     def doReproj      = task.ext.args?.getAt("DO_REPROJ")              ? "DO_REPROJ = ${task.ext.args["DO_REPROJ"]}"                         : "DO_REPROJ = TRUE"
     def doTile        = task.ext.args?.getAt("DO_TILE")                ? "DO_TILE = ${task.ext.args["DO_TILE"]}"                             : "DO_TILE = TRUE"
     def fileTile      = tile                                           ? "FILE_TILE = $tile"                                                 : "FILE_TILE = NULL"
     // "TILE_SIZE"    can only be set after input stage-in
-    // "BLOCK_SIZE"   can only be set after input stage-in
     def landsatRes    = task.ext.args?.getAt("RESOLUTION_LANDSAT")     ? "RESOLUTION_LANDSAT = ${task.ext.args["RESOLUTION_LANDSAT"]}"       : "RESOLUTION_LANDSAT = 30"
     def sentinel2Res  = task.ext.args?.getAt("RESOLUTION_SENTINEL2")   ? "RESOLUTION_SENTINEL2 = ${task.ext.args["RESOLUTION_SENTINEL2"]}"   : "RESOLUTION_SENTINEL2 = 10"
     // "ORIGIN_LON    can only be set after input stage-in
@@ -150,7 +151,6 @@ process FORCE_PREPROCESS {
     ORIGINX=\$(sed '2q;d' $cube)
     ORIGINY=\$(sed '3q;d' $cube)
     TILESIZE=\$(sed '6q;d' $cube)
-    BLOCKSIZE=\$(sed '7q;d' $cube)
 
     # create parameter file
     PARAM=./preprocess_${data.simpleName}.prm
@@ -165,11 +165,12 @@ process FORCE_PREPROCESS {
     ${fileAoi}
     FILE_DEM = \$DEM_FILE
     ${demNoData}
+    ${useDemDB}
+    ${demResampling}
     ${doReproj}
     ${doTile}
     ${fileTile}
     TILE_SIZE = \$TILESIZE
-    BLOCK_SIZE = \$BLOCKSIZE
     ${landsatRes}
     ${sentinel2Res}
     ORIGIN_LON = \$ORIGINX

diff --git a/modules/local/force-pyramid/main.nf b/modules/local/force-pyramid/main.nf
@@ -2,7 +2,7 @@ process FORCE_PYRAMID {
     tag { meta.id }
     label 'process_low'
 
-    container "nf-core/force:3.8.01"
+    container "nf-core/force:3.10.04"
 
     input:
     tuple val(meta), path(image)

diff --git a/modules/local/merge/main.nf b/modules/local/merge/main.nf
@@ -3,7 +3,7 @@ process MERGE {
     label 'process_low'
     label 'error_retry'
 
-    container "nf-core/force:3.8.01"
+    container "nf-core/force:3.10.04"
 
     input:
     val (data_type) // defines whether qai or boa is merged

diff --git a/nf-test.config b/nf-test.config
@@ -19,6 +19,6 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "nft-utils@0.0.3"
+        load "nft-utils@0.0.9"
     }
 }