Copy or move the files instead of creating symlinks in the LocalizeReads task for compatibility with CoA/TES.

[VJalili]

The task LocalizeReads creates symlinks for the localized cram and its corresponding index file in the current working directory to simplify referencing them in the task output. Specifically, the files are localized in the following directory, and symlinks are created in the /cromwell_root/.

/cromwell_root/…/analysis/filename.cram

Symlinks as this are incompatible with GA4GH TES and Cromwell on Azure.

Therefore, this PR updates the script to move or copy the files instead of creating symlinks. Moving files (mv) is faster and requires less disk space on the VM than copying the files. However, run on HPC, moving files could lead to moving them from their source directory compared to moving them from the localized directory to the root directory on the VM. Therefore, we provide both options for moving and copying to avoid moving files unexpectedly and set the copy as default.

Cromwell submission ID for a successful test of this PR is bd10381c-53b3-4c67-a396-291135af0f6f.

The following can be an alternative to moving the files, though it still needs to be tested.

File output_file = basename(reads_path)  --> File output_file = reads_path

[mwalker174]

Thanks @VJalili! Did you happen to test using cp as well? We've had complaints in the past about moving mv on input files from folks using shared filesystems. I realize it's slower and would require extra disk, but I would think that the cost would be small.

[VJalili]

That is a good point, thank you, @mwalker174.

Yes, I first tested using cp, but it failed with an out-of-disk error, so I tried with mv. I think this is moving a file localized to a directory on the runner's VM to another directory on the VM. I think even when using a shared file system, this VM still has its own copy/localized version of the file, so it should not be moving a file on a different file system. Though I have not tested, and am happy to test, I will only need some references to files on the shared file system.

[mwalker174]

Looks good! Minor comments

[VJalili]

Thank you, @mwalker174!!