[Swift-user] Management of undeclared files

[Aurélien Mazurie]

Dear all,
After making my way through the Swift documentation I started writing test workflows to see how simple (then more complex) tasks would be managed by this platform. One such test workflow is giving me issues, and I couldn't find an obvious solution in the documentation.

I wrote this script, http://pastebin.com/zQZQphCd <http://pastebin.com/zQZQphCd> to format a FASTA file using the NCBI BLAST utility makeblastdb. What is interesting is that although the Swift script run without error, I cannot find the files makeblastdb is meant to produce anywhere on my hard drive.

I do get the correct log file (log_file variable), and this log shows that makeblastdb ran successfully. However I should also get three other files, <library_name>.nin, <library_name>.nhr and <library_name>.nsq.

My question is: where are these files? Since makeblastdb ran without issue, they probably have been created somewhere (and I confirm that they are created when I run the exact same  command on the terminal). Are they automatically deleted by Swift since they are not explicitly named by another variable?

I'm guessing that the answer is yes; if that the case, is there a way to have variables storing file names that are only known at execution time? For example, I would like my 'FormatLibrary' function to return among else the name of these three files, rather than having to bind these file names to variables before the execution of this function. Is that even doable?

Best,
Aurélien Mazurie
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/swift-user/attachments/20150610/01899dd2/attachment.html>