Add a workaround for symlinked file handling.

[sclan]

SF15975

Andrew from St. Jude can't download the symlinked data for running their wdl workflow on platform, and the streaming option degraded the performance quite a bit (samtools index does not work well with data streaming). To avoid the issue, another workaround is to download the input with old fashioned dx download command and I have added the information for the documentation puporse in this PR.