Short wf outputs issue

[TimSPb89]

Issue

Short syntax in workflow output section causes application to throw an Error:

Script to reproduce:

#Onctotator Task
task OncotatorTask {
  File inputMAFLite

  command {
    ################################################################
    #Oncotator
    oncotator --db-dir /cga/fh/pcawg_pipeline/modules/oncotator/empty  -o VCF ${inputMAFLite} SAMPLE.vcf hg19
    }

  output {
    File oncotatorVCF="SAMPLE.vcf"
  }

  runtime {
    docker: "eddiebroad/contest_mutect_oncotator"
    memory: "24 GB"
    defaultDisks: "local-disk 100 SSD"
  }
}

workflow ContEstMuTect {
  #Oncotator inputs
  File inputMAFLite

  #call oncotator
  call OncotatorTask {
    input: inputMAFLite=inputMAFLite
  }

  output {
    OncotatorTask.oncotatorVCF
  }  
}

Changes

This PR resolves this issue

[coveralls]

Coverage increased (+0.08%) to 97.205% when pulling 25b4900 on short-wf-outputs-issue into 85a88c5 on dev.