Variables in task output

golharamgolharam Member ✭✭✭

Hi - I'm starting to learn WDL/Cromwell, so forgive me if my questions are a naive. I'm working on my first "real" pipeline. I'm getting this error when trying to generate the input json file:

Unrecognized token on line 27, column 26:

    String output_path = ${run_folder}-output

The task this line is in, is :

task cellranger_mkfastq {
  String run_folder

  command {
    cellranger mkfastq \
      --id ${run_folder}-output \
      --run=/scratch/${run_folder} \
      --samplesheet=/scratch/${run_folder}/SampleSheet.csv \
      --qc
  }

  output {
    String output_path = ${run_folder}-output
  }
}

Line 27 is "String output_path = ${run_folder}-output"

What is wrong with this line? Can variables not be used in the output section?

Answers

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