gz handling in WDL 1.0

task example {
  input {
    File fasta_or_fasta_gz
  }

  String uncompressed_fasta = basename(fasta_or_fasta_gz, ".gz")

  command <<<
    set -exuo pipefail
    uncompress() {  # uncompress source dest
      if [ "$(basename "${1}")" = "$2" ]; then
        cp "${1}" "${2}"
      else
        gunzip --stdout "${1}" > "${2}"
      fi
    }
    uncompress '~{fasta_or_fasta_gz}' '~{uncompressed_fasta}'
    samtools faidx '~{uncompressed_fasta}'
  >>>

  output {
    File fasta = uncompressed_fasta
    File fasta_index = uncompressed_fasta + '.fai'
  }
}