How do I rename output folder created using WDL's glob function, with cromwell execution engine?
Ok, thanks to Ruben Vorderman on the openwdl github page, I found a solution that does not involve renaming the glob folder (which I believe is not possible?). The only way is to write out the names of the files and pass them explicitly to the Array[File] output. This is how I did it (simplified), in case it helps anyone else in the future:
task fastqc_task {
  File forwardReads
  File reverseReads
  String fwdName = sub(basename(forwardReads),&quot;.f.*q.*$","")
  String revName = sub(basename(reverseReads),".f.*q.*$&quot;,&quot;&quot;)
  command {
    mkdir -p ./qc/fastqc_zip
    fastqc ${forwardReads} ${reverseReads} --outdir ./qc/fastqc_zip
  }
  output {
    Array[File] fastqcArray = [&quot;./qc/fastqc_zip/${fwdName}_fastqc.zip", "./qc/fastqc_zip/${revName}_fastqc.zip&quot;]
  } 
}