qsv output directory is specified on INI file [general] section, it also creates a UUID as a subfolder to store the output files. In the previous version, there is a command-line option "--overrideOutput", qsv will create or overwrite outputs to that directory; and ignore the INI file option "output" under [general] section.
In the new version, a new option "--uuid" replaced the previous "--overrideOutput". This "--uuid" specifies the subfolder name. Here the INI file option "output" won't ignored, it is the parent folder of the "--uuid" folder. We must check whether the INI "output" directory exists or not, disregards with/without command-line option "--uuid".
Type of change
Please delete options that are not relevant.
[X] Bug fix (non-breaking change which fixes an issue)
How Has This Been Tested?
Unit test is added; It also runs on a real dataset, with a different "output" value in the INI file. The output location is hpcpbs01:/mnt/lustre/working/genomeinfo/share/testdataXu/qsv/20210716.
Are WDL Updates Required?
not affect any WDL
Checklist:
[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes
Description
qsv output directory is specified on INI file [general] section, it also creates a UUID as a subfolder to store the output files. In the previous version, there is a command-line option "--overrideOutput", qsv will create or overwrite outputs to that directory; and ignore the INI file option "output" under [general] section.
In the new version, a new option "--uuid" replaced the previous "--overrideOutput". This "--uuid" specifies the subfolder name. Here the INI file option "output" won't ignored, it is the parent folder of the "--uuid" folder. We must check whether the INI "output" directory exists or not, disregards with/without command-line option "--uuid".
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Unit test is added; It also runs on a real dataset, with a different "output" value in the INI file. The output location is hpcpbs01:/mnt/lustre/working/genomeinfo/share/testdataXu/qsv/20210716.
Are WDL Updates Required?
not affect any WDL
Checklist: