The features of this PR primarily concerns internals.
End-users:
Responsible bioinformatician added to both logs and final report
Json output reports now default to '' (empty) for non-standard values
Bioinformatics:
Reports aren't removed from current folder, if a report is already present
Internal:
The index checker for blast databases is now more thorough
BLAST searches generalized to single function
EXPAC set correctly renamed to ExPEC
Optimized loci-length checker
Fixed oversights in verified_fastq function, and database indexes when using parse_seqids
CSV files are now readable regardless of language version
Kmer coverage is used as a tertiary sorter if identity and span are otherwise identical
Fixed an issue where some characters were incorrectly displayed when printing a report
Input fastq are now verified to not end improperly
The reason for packaging these features is due to shifting focus in development, and packaging them avoids the code from becoming legacy/forgotten/useless.
Primary function of PR
[ ] Hotfix
[X] Patch
[x] Minor functionality improvement
[ ] New type of analysis
[ ] Backward-breaking functionality improvement
[ ] This change requires internal documents to be updated
[ ] This change requires another repository to be updated
Testing
This is a description of the tests necessary to verify the stability of the PR.
_Verify that the results for projects MIC3109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx
Additionally:
Make sure responsible bioinformatician is written within the Typing & QC reports
Use microSALT utils report <PROJECT> --type json_dump and verify that the non-standard values (like Control) are written as empty
Use microSALT utils report <PROJECT> --type default --output . twice to verify that the report isn't removed
Test results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR.
MIC3109 - QC: Coverage based metrics offset by less than 5%. Otherwise identical
ACC5551 - Typing results: Convergent
ACC5551 - Resistance results: Convergent
Running microSALT utils report <PROJECT> --type json_dump for project MIC3109 & ACC5551 produces json files where multiple values are ''; such as n50 and duplication_rate for project MIC3109.
Running microSALT utils report <PROJECT> --type default --output . twice still left the reports intact.
Sign-offs
[X] Code reviewed by @sylvinite
[X] Code tested by @sylvinite
[X] Approved to run at Clinical-Genomics by @ingkebil
Description
The features of this PR primarily concerns internals.
End-users:
Bioinformatics:
Internal:
The reason for packaging these features is due to shifting focus in development, and packaging them avoids the code from becoming legacy/forgotten/useless.
Primary function of PR
Testing
This is a description of the tests necessary to verify the stability of the PR.
bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh json_fix_ussource activate S_microSALT_microSALT analyse project MIC3109microSALT analyse project ACC5551_Verify that the results for projects MIC3109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx
Additionally:
microSALT utils report <PROJECT> --type json_dumpand verify that the non-standard values (like Control) are written as emptymicroSALT utils report <PROJECT> --type default --output .twice to verify that the report isn't removedTest results
These are the results of the tests, and necessary conclusions, that prove the stability of the PR.
MIC3109 - QC: Coverage based metrics offset by less than 5%. Otherwise identical ACC5551 - Typing results: Convergent ACC5551 - Resistance results: Convergent
Running
microSALT utils report <PROJECT> --type json_dumpfor project MIC3109 & ACC5551 produces json files where multiple values are ''; such as n50 and duplication_rate for project MIC3109. RunningmicroSALT utils report <PROJECT> --type default --output .twice still left the reports intact.Sign-offs