Pass path to logo to template generator

public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/pdf_report.py

@@ -84,7 +84,7 @@ def natural_sort(inlist):
     return inlist
 
 
-def write_template(summary_file, template_file):
+def write_template(summary_file, template_file, logo_file):
 
     template_file = path.abspath(path.realpath(template_file))
     template_dir = path.dirname(template_file)
@@ -112,7 +112,7 @@ def write_template(summary_file, template_file):
     render_vars = {
         "gentrap": {
             "version": "--testing--",
-            "logo": "/home/warindrarto/devel/intellij/biopet/public/gentrap/src/main/resources/nl/lumc/sasc/biopet/pipelines/gentrap/templates/img/gentrap_front.png",
+            "logo": logo_file,
         },
     }
     rendered = jinja_template.render(**render_vars)
@@ -127,6 +127,8 @@ if __name__ == "__main__":
             help="Path to Gentrap summary file")
     parser.add_argument("template_file", type=str,
             help="Path to main template file")
+    parser.add_argument("logo_file", type=str,
+            help="Path to main logo file")
     args = parser.parse_args()
 
-    write_template(args.summary_file, args.template_file)
+    write_template(args.summary_file, args.template_file, args.logo_file)

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/PdfReportTemplateWriter.scala

@@ -21,6 +21,7 @@ class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineF
 
   val templateResDir: File = new File(getClass.getResource("/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf").toURI)
   val templateWorkDir: File = new File(".queue/tmp/nl/lumc/sasc/biopet/pipelines/gentrap/templates/pdf")
+  val imgWorkDir: File = new File(templateWorkDir, "img")
 
   @Input(doc = "Input summary file", required = true)
   var summaryFile: File = null
@@ -28,6 +29,9 @@ class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineF
   @Input(doc = "Main report template", required = true) // def since we hard-code the template
   def mainTemplateFile: File = new File(templateWorkDir, "main.tex")
 
+  @Input(doc = "Main report logo", required = true) // def since we hard-code the logo
+  def logoFile: File = new File(imgWorkDir, "gentrap_front.png")
+
   @Output(doc = "Output file", required = true)
   var output: File = null
 
@@ -39,6 +43,7 @@ class PdfReportTemplateWriter(val root: Configurable) extends PythonCommandLineF
     getPythonCommand +
       required(summaryFile) +
       required(mainTemplateFile) +
+      required(logoFile.getAbsoluteFile) +
       " > " + required(output)
   }