Variable is already defined when file content relative to baseDir is stored in a def

[billencamper]

I am currently setting up a subroutine to check my pipeline parameters and provide an extended usage information upon missing parameters.

                            if(!params.fastqfolder||!params.metadata||!params.species){
                                  def myoutput= file("${baseDir}/res/Help.txt").text
 			          checkresult=false
	 	            }

-->This throws an Error:
ERROR ~ Module compilation error

• file : $PATH_TO_BASEDIR/./bin/Setup.nf

• cause: Variable baseDir already defined in the process scope @ line 58, column 28.

• Line 58 is def myoutput= file("${baseDir}/res/Help.txt").text

                      if(!params.fastqfolder||!params.metadata||!params.species){
                                 println file("${baseDir}/res/Help.txt").text
    		               checkresult=false
     	            }
  

-->This runs fine

Since I would like to color the output, I would need adjust myoutput by adding ANSI.
e.g. the following works like a charm.

println ("\u001B[32mNo outfolder provided.\nOutput will be stored in folder Output next to the pipeline script\u001B[0m")

Currently I do not see what could be wrong before I even reach the ANSI. As for my understanding I do not define baseDir anywhere but only use it in a relative path.
baseDir does not occur in Help.text, no $baseDir in that file either.

[bentsherman]

Is this code happening inside a function? or a process? or the main script?

Also, you can try using workflow.projectDir instead of baseDir, they are identical and the former is preferred.

[billencamper]

I have a main.nf and a setup.nf in folder $baseDir/bin

Code is happening inside exec: - block of a process in setup that is used to check params for flags and required input.

Problem is not that I cannot access via $baseDir, but that a String inside a file in "$baseDir/res/Help.txt" can be accessed via println file("${baseDir}/res/Help.txt").text without problems, however, if i try to store the String in a def via def storedstring= file("${baseDir}/res/Help.txt").text I get the baseDir is allready defined crash.

[bentsherman]

Can you provide a more complete example? I tried to create one from your code snippet but I can't reproduce it.