Merge pull request #9 from CRC-FONDA/dev

Adressing review suggestions for Version 1.0.0

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test*

.nf-core.yml

@@ -2,6 +2,7 @@ bump_version: null
 lint:
   files_exist:
     - conf/igenomes.config
+    - conf/igenomes_ignored.config
 nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline

CHANGELOG.md

@@ -5,7 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.0.0 - [date]
 
-Initial release of nf-core/rangeland, created with the [nf-core](https://nf-co.re/) template.
+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`
 

README.md

@@ -19,7 +19,8 @@
 
 ## Introduction
 
-**nf-core/rangeland** is a geographical best-practice 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:
+**nf-core/rangeland** is a geographical best-practice 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, endmember definition, water vapor database and area of interest definition
 2. Generate allow list and analysis mask to determine which pixels from the satellite data can be used
@@ -28,20 +29,22 @@
 5. Time series analyses to obtain trends in vegetation dynamics
 6. Create mosaic and pyramid visualizations of the results
 
-7. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-8. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+7. Present QC results ([`MultiQC`](http://multiqc.info/))
 
 ## Usage
 
 > [!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.
+> 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 the pipeline on real data, input data needs to be acquired. Concretely, satellite imagery, water vapor data, a digital elevation model, endmember definitions, a datacube specification, and a area-of-interest specification are required. Please refer to the [usage documentation](https://nf-co.re/rangeland/usage) for details on the input structure.
+To run the pipeline on real data, input data needs to be acquired.
+Concretely, satellite imagery, water vapor data, a digital elevation model, endmember definitions, a datacube specification, and a area-of-interest specification are required.
+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/main.nf \
+nextflow run nf-core/rangeland \
    -profile <docker/singularity/.../institute> \
    --input <SATELLITE IMAGES> \
    --dem <DIGITAL ELEVATION MODEL> \
@@ -72,7 +75,8 @@ The rangeland workflow was originally written by:
 
 The original workflow can be found on [github](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland).
 
-Transformation to nf-core/rangeland was conducted by [Felix Kummer](https://github.com/Felix-Kummer). nf-core alignment started on the [nf-core branch of the original repository](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland/tree/nf-core).
+Transformation to nf-core/rangeland was conducted by [Felix Kummer](https://github.com/Felix-Kummer).
+nf-core alignment started on the [nf-core branch of the original repository](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland/tree/nf-core).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -114,7 +118,8 @@ You can cite the `nf-core` publication as follows:
 >
 > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
 
-This pipeline is based one the publication listed below. The publication can be cited as follows:
+This pipeline is based one the publication listed below.
+The publication can be cited as follows:
 
 > **FORCE on Nextflow: Scalable Analysis of Earth Observation Data on Commodity Clusters**
 >

bin/merge_boa.r

@@ -1,44 +1,46 @@
 #!/usr/bin/env Rscript
 
-args = commandArgs(trailingOnly=TRUE)
+## Originally written by Felix Kummer and released under the MIT license.
+## See git repository (https://github.com/nf-core/rangeland) for full license text.
 
+# Script for merging bottom of atmosphere (boa) .tif raster files.
+# This can improve the performance of downstream tasks.
 
-if (length(args) < 3) {
-    stop("\nthis program needs at least 3 inputs\n1: output filename\n2-*: input files", call.=FALSE)
-}
-
-fout <- args[1]
-finp <- args[2:length(args)]
-nf <- length(finp)
-
-require(raster)
-
-
-img <- brick(finp[1])
-nc <- ncell(img)
-nb <- nbands(img)
+require(terra)
 
+args <- commandArgs(trailingOnly = TRUE)
 
-sum <- matrix(0, nc, nb)
-num <- matrix(0, nc, nb)
-
-for (i in 1:nf){
-
-    data <- brick(finp[i])[]
-
-    num <- num + !is.na(data)
-
-    data[is.na(data)] <- 0
-    sum <- sum + data
 
+if (length(args) < 3) {
+    stop("\nError: this program needs at least 3 inputs\n1: output filename\n2-*: input files", call.=FALSE)
 }
 
-mean <- sum/num
-img[] <- mean
-
+fout <- args[1]
+finp <- args[2:length(args)]
 
-writeRaster(img, filename = fout, format = "GTiff", datatype = "INT2S",
-            options = c("INTERLEAVE=BAND", "COMPRESS=LZW", "PREDICTOR=2",
-            "NUM_THREADS=ALL_CPUS", "BIGTIFF=YES",
-            sprintf("BLOCKXSIZE=%s", img@file@blockcols[1]),
-            sprintf("BLOCKYSIZE=%s", img@file@blockrows[1])))
+# Load input rasters
+rasters <- lapply(finp, rast)
+
+# Calculate the sum of non-NA values across all rasters
+sum_rasters <- Reduce("+", lapply(rasters, function(x) {
+    x[is.na(x)] <- 0
+    return(x)
+}))
+
+# Calculate the number of values non-NA values for each cell
+count_rasters <- Reduce("+", lapply(rasters, function(x) {
+    return(!is.na(x))
+}))
+
+# Calculate the mean raster
+mean_raster <- sum_rasters / count_rasters
+
+# Write the mean raster
+writeRaster(mean_raster,
+            filename = fout,
+            datatype = "INT2S",
+            filetype = "GTiff",
+            gdal     = c("COMPRESS=LZW", "PREDICTOR=2",
+                        "NUM_THREADS=ALL_CPUS", "BIGTIFF=YES",
+                        sprintf("BLOCKXSIZE=%s", ncol(mean_raster)),
+                        sprintf("BLOCKYSIZE=%s", nrow(mean_raster))))

bin/merge_qai.r

@@ -1,38 +1,41 @@
 #!/usr/bin/env Rscript
 
-args = commandArgs(trailingOnly=TRUE)
+## Originally written by Felix Kummer and released under the MIT license.
+## See git repository (https://github.com/nf-core/rangeland) for full license text.
 
+# Script for merging quality information (qai) .tif raster files.
+# This can improve the performance of downstream tasks.
 
-if (length(args) < 3) {
-    stop("\nthis program needs at least 3 inputs\n1: output filename\n2-*: input files", call.=FALSE)
-}
-
-fout <- args[1]
-finp <- args[2:length(args)]
-nf <- length(finp)
-
-require(raster)
-
-
-img <- raster(finp[1])
-nc <- ncell(img)
+require(terra)
 
+args <- commandArgs(trailingOnly = TRUE)
 
-last <- rep(1, nc)
-
-for (i in 1:nf){
-
-    data <- raster(finp[i])[]
-
-    last[!is.na(data)] <- data[!is.na(data)]
 
+if (length(args) < 3) {
+    stop("\nError: this program needs at least 3 inputs\n1: output filename\n2-*: input files", call.=FALSE)
 }
 
-img[] <- last
-
+fout <- args[1]
+finp <- args[2:length(args)]
 
-writeRaster(img, filename = fout, format = "GTiff", datatype = "INT2S",
-            options = c("INTERLEAVE=BAND", "COMPRESS=LZW", "PREDICTOR=2",
-            "NUM_THREADS=ALL_CPUS", "BIGTIFF=YES",
-            sprintf("BLOCKXSIZE=%s", img@file@blockcols[1]),
-            sprintf("BLOCKYSIZE=%s", img@file@blockrows[1])))
+# load raster files into single SpatRaster
+rasters <- rast(finp)
+
+# Merge rasters by maintaining the last non-NA value
+merged_raster <- app(rasters, function(x) {
+    non_na_values <- na.omit(x)
+    if (length(non_na_values) == 0) {
+        return(1)
+    }
+    return(tail(non_na_values, 1)[1])
+})
+
+# Write merged raster
+writeRaster(merged_raster,
+            filename = fout,
+            filetype = "GTiff",
+            datatype = "INT2S",
+            gdal     = c("INTERLEAVE=BAND", "COMPRESS=LZW", "PREDICTOR=2",
+                        "NUM_THREADS=ALL_CPUS", "BIGTIFF=YES",
+                        sprintf("BLOCKXSIZE=%s", ncol(merged_raster)),
+                        sprintf("BLOCKYSIZE=%s", nrow(merged_raster))))

bin/test.R

@@ -1,5 +1,10 @@
 #!/usr/bin/env Rscript
 
+## Originally written by David Frantz and Felix Kummer and released under the MIT license.
+## See git repository (https://github.com/nf-core/rangeland) for full license text.
+
+# Script to verify pipeline results from test and test_full profiles.
+
 args = commandArgs(trailingOnly=TRUE)
 
 
@@ -116,21 +121,6 @@ peak_year_of_change <- peak_rast["YEAR-OF-CHANGE"]
 
 
 
-# FOR REFERENCE: SAVE RASTERS
-#######################################################################
-
-#writeRaster(woody_cover_changes,        "woody_cover_chg_ref.tif")
-#writeRaster(woody_cover_year_of_change, "woody_cover_yoc_ref.tif")
-
-#writeRaster(herbaceous_cover_changes,        "herbaceous_cover_chg_ref.tif")
-#writeRaster(herbaceous_cover_year_of_change, "herbaceous_cover_yoc_ref.tif")
-
-#writeRaster(peak_changes,        "peak_chg_ref.tif")
-#writeRaster(peak_year_of_change, "peak_yoc_ref.tif")
-
-
-
-
 # COMPARE TESTRUN WITH REFERENCE EXECUTION
 #######################################################################
 failure <- FALSE

conf/base.config

@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }