add params.publish_generated_img

Author: dannda

main.nf

@@ -16,6 +16,7 @@ params.outdir = ""
 params.args = [:]
 params.projects = []
 params.write_spatialdata = false
+params.publish_generated_img = false
 
 params.vitessce_options = [:]
 params.layout = "minimal"
@@ -250,7 +251,7 @@ process Generate_image {
     tag "${stem}, ${img_type}, ${file_path}"
     debug verbose_log
 
-    publishDir outdir_with_version, mode: "copy"
+    publishDir outdir_with_version, mode: "copy", enabled: params.publish_generated_img
 
     input:
     tuple val(stem), val(prefix), val(img_type), path(file_path), val(file_type), path(ref_img), val(args)

sphinx/configuration.rst

@@ -133,7 +133,9 @@ The more detailed list of parameters is as follows:
     * - ``outdir``
       - the path to the directory to which output files will be written.
     * - ``write_spatialdata``
-      - ``true`` or ``false``, if processed datasets should also get each written to `SpatialData <https://spatialdata.scverse.org/en/latest/index.html>`_
+      - ``true`` or ``false``, if processed datasets should also get each written to `SpatialData <https://spatialdata.scverse.org/en/latest/index.html>`_ . Defaults to ``false``.
+    * - ``publish_generated_img``
+      - ``true`` or ``false``, if the pipeline should publish generated images' ``.tif`` files to the output directory. Defaults to ``false``.
     * - ``args``
       - a map of optional arguments per data type for the scripts that process them.