From 8a4179055e66bdf684d23561f72060ee80e25a52 Mon Sep 17 00:00:00 2001
From: TcFigSCD <t.figueiredo@scdiscoveries.com>
Date: Thu, 12 Mar 2026 16:54:51 +0100
Subject: [PATCH 1/2] Added new module for image conversion

---
 modules/local/utility/image_converter/main.nf | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 modules/local/utility/image_converter/main.nf

diff --git a/modules/local/utility/image_converter/main.nf b/modules/local/utility/image_converter/main.nf
new file mode 100644
index 00000000..e831bb1c
--- /dev/null
+++ b/modules/local/utility/image_converter/main.nf
@@ -0,0 +1,45 @@
+process IMAGE_COVERTER{
+    
+    tag "IMAGE_COVERTER"
+    
+    publishDir "${params.outdir}/images", mode: 'copy'
+    
+    container "docker://labsyspharm/bftools:latest"
+    
+    memory = '50.GB'
+    cpus = 10
+
+    input:
+    path (omi_tif_image)
+    val (extension)
+
+    output:
+    path ("bfconvert_output"), emit: converted_images
+    path ("versions.yml"), emit: versions
+    
+    when:
+    task.ext.when == null || task.ext.when
+    
+    script:
+    
+    def args = task.ext.args ?: ''
+    
+    """
+    # Increase heap memory used by JVM inside the container to avoid OutOfMemoryError
+    # Should be set according to the amount of memonry allocated to the module
+    export BF_MAX_MEM=50g
+    
+    # Create output directory for bfconvert results
+    mkdir bfconvert_output
+    
+    # Run bfconvert with the specified parameters
+    bfconvert \\
+        $args \\
+        ${omi_tif_image} bfconvert_output/output_series_%s_Z%z.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bftools: \$(echo \$(bfconvert -version 2>&1) | sed 's/^.*Version: //; s/ Build.*\$//')
+    END_VERSIONS
+    """
+}
\ No newline at end of file

From ed35f16014296817b8da9a5403cf842dbf79ba58 Mon Sep 17 00:00:00 2001
From: TcFigSCD <t.figueiredo@scdiscoveries.com>
Date: Fri, 13 Mar 2026 11:26:32 +0100
Subject: [PATCH 2/2] Added stub to module

---
 modules/local/utility/image_converter/main.nf | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/modules/local/utility/image_converter/main.nf b/modules/local/utility/image_converter/main.nf
index e831bb1c..380ff5a7 100644
--- a/modules/local/utility/image_converter/main.nf
+++ b/modules/local/utility/image_converter/main.nf
@@ -21,9 +21,7 @@ process IMAGE_COVERTER{
     task.ext.when == null || task.ext.when
     
     script:
-    
     def args = task.ext.args ?: ''
-    
     """
     # Increase heap memory used by JVM inside the container to avoid OutOfMemoryError
     # Should be set according to the amount of memonry allocated to the module
@@ -33,6 +31,7 @@ process IMAGE_COVERTER{
     mkdir bfconvert_output
     
     # Run bfconvert with the specified parameters
+    # The command for now only works by converting the .ome.tiff image into several .png files.
     bfconvert \\
         $args \\
         ${omi_tif_image} bfconvert_output/output_series_%s_Z%z.${extension}
@@ -42,4 +41,15 @@ process IMAGE_COVERTER{
         bftools: \$(echo \$(bfconvert -version 2>&1) | sed 's/^.*Version: //; s/ Build.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir bfconvert_output
+    touch bfconvert_output/output_series_0_Z0.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bftools: \$(echo \$(bfconvert -version 2>&1) | sed 's/^.*Version: //; s/ Build.*\$//')
+    END_VERSIONS
+    """
 }
\ No newline at end of file