Add option to upload compressed files

[colinbrislawn]

Scenario:

Currently, --local-compress only compresses the file passed in --local-save, but the file uploaded are not compressed. I would like an option to upload a compressed files.

Steps to Reproduce:

pacifica-cli upload --proposal 0 --local-save folder.tar.gz --local-compress gzip folder/

Expected Result:

folder.tar.gz is uploaded into datahub

Actual Result:

The contents of folder/ are uploaded, without compression.

[dmlb2000]

The --local options are for how to manipulate the data locally, not what goes into Pacifica. The option to bundle your data for you and put a single file into Pacifica is the --tar-in-tar option.

Would adding an argument to --tar-in-tar be workable to compress the file put into Pacifica? (i.e. --tar-in-tar=gzip)

[colinbrislawn]

Currently, I really like being able to see each individual sample file, so I don't plan to use --tar. I think simply gzipping all the fastq files, while redundant for /pic/projects/, is the most elegant solution.

I like the idea of --tar-in-tar=gzip, but my use case doesn't need it.

Feel free to close this issue. 👍