Add ubuntu group to ubuntu user in cwl-runner's docker command

[Jeltje]

Feature request

Currently, when I run
cwl-runner tool.cwl tool.json
The docker command contains this:

    --user=1000 \

This results in my files being owned by user ubuntu in group root:
-rw-r--r-- 1 ubuntu root 824831998 Jan 4 20:16 dbSNP_chr17.vcf

Using --user=1000:1000 will create the correct group:
-rw-r--r-- 1 ubuntu ubuntu 104046759 Jan 4 20:17 dbSNP_chr17.vcf.gz

Can this be changed?

[manu-chroma]

A very straightforward fix will be to change this string: https://github.com/common-workflow-language/cwltool/blob/master/cwltool/job.py#L400

But I am not very sure how UID works.

[mr-c]

1. get the "egid" (effective group ID), just like in https://github.com/common-workflow-language/cwltool/blob/master/cwltool/job.py#L394
2. change https://github.com/common-workflow-language/cwltool/blob/master/cwltool/job.py#L400
   to
   runtime.append(u"--user=%s:%s" % (euid, egid))