Add image converter module - issue #22

modules/local/utility/image_converter/main.nf

@@ -0,0 +1,55 @@
+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
+    # 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}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bftools: \$(echo \$(bfconvert -version 2>&1) | sed 's/^.*Version: //; s/ Build.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir bfconvert_output
+    touch bfconvert_output/output_series_0_Z0.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bftools: \$(echo \$(bfconvert -version 2>&1) | sed 's/^.*Version: //; s/ Build.*\$//')
+    END_VERSIONS
+    """
+}