Asma

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Asma
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Member, Broadie
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  • filter_basename=${basename(filter_input)}, does not work, pipeline doesn't even begin to run. I have tried the following line filter_basename=${basename $(filter_input)}, though the pipeline starts; it errors out in command section at line O=UMI_DG…
  • This is what the task looks like now: task DigitalExpressionUMI { String dropseq_home String java_memory String filter_input Int umi_edit_distance String cell_tag_collapsed String barcodes command { mkdir "UMI_DGE" filter_basename=$(ba…
  • I figured out the correct syntax of basename, it should be filter_basename=$(basename ${filter_input}). I was missing a "$" before basename. I am running a test to see if it works.
  • Which Cromwell version are you using? - cromwell-28_2.jar Which backend are you using? - Using a LINUX server Are you running your own Cromwell or is somebody else hosting it? If it's your own, is it in server or run mode? Using own Cromwell in ru…