local docker permissions problems

I have to start cromwell with sudo to be able to run anything in docker. In the same time when I start cromwell as sudo it creates all folders with root privileges and I have things like: /bin/bash: /root/bedtest/7702b69d-25ac-4d3e-964c-be15181a59c5/call-coverage/execution/script: Permission denied in stderr.

Here is the WDL that I run:

workflow bedtest {

  File first
  File second

  call coverage {
    input:first=first,second=second
  }
}

task coverage {

  File first
  File second

  command {
    bedtools coverage -sorted -a $first -b $second -counts > counts.txt
  }

  runtime {
    docker: "biocontainers/bedtools"
  }

  output {
    File counts = "counts.txt"
  }
}

Here are the inputs that I pass through API:

JSONObject(
    "bedtest.first" -> "/home/antonkulaga/data/assembly4/4_sorted.bam",
    "bedtest.second" -> "/home/antonkulaga/data/assembly4/9_sorted.bam"
  )

P.S. I also tried:

sudo usermod -aG docker $USER

that allows to run docker without sudo. The problem remains the same.

[antonkulaga]

In the latest version docker works like a charm, thank you for fixing this!

[geoffjentry]

Perfect, thanks for the update