_Verify that the results for project ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx
Additionally, use the reports commands to generate the different type of reports; with and without an output directory. Make sure report files appear locally and in the REPORTS directory as to be expected.
Test results
Results for ACC5551 are consistent with prior results.
Reports are generated in subdirectories of the reports directory of the configuration.
Using --output correctly puts a copy of reports in that directory.
Sign-offs
[x] Code tested by @sylvinite
[ ] Approved to run at Clinical-Genomics by @sylvinite
Description
The features of this PR primarily concerns bioinformaticians
Reports are now explicitly stored in the reports folder, and subfolders thereof. Furthermore files are then copied from there, to the local space.
This change is necessary as both Vogue and software CG expects json files in very specific folders to operate successfully.
Primary function of PR
Testing
Test routine to verify the stability of the PR:
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh fix_reportfolder_ussource activate S_microSALT_microSALT analyse project ACC5551_Verify that the results for project ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx
Additionally, use the reports commands to generate the different type of reports; with and without an output directory. Make sure report files appear locally and in the REPORTS directory as to be expected.
Test results
Results for ACC5551 are consistent with prior results. Reports are generated in subdirectories of the reports directory of the configuration. Using --output correctly puts a copy of reports in that directory.
Sign-offs