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Microsalt does not handle missing alleles

bug

Status: Open.

#254 In Clinical-Genomics/microSALT;

· eliottBo opened on Jul 14, 2026

Issues in microSALT storing has resulted in many analysis obj in StatusDB having the incorrect workflow version 0.0.0

Status: Open.

#200 In Clinical-Genomics/microSALT;

· karlnyr opened on Mar 12, 2025

ST_profiles from pubMLST not updating

bug

Status: Open.

#197 In Clinical-Genomics/microSALT;

· eliottBo opened on Mar 10, 2025

Change the number of reads used in the QC report to the total number of reads, not the number of reads after filtering

Status: Open.

#196 In Clinical-Genomics/microSALT;

· karlnyr opened on Jan 22, 2025

Issue with reporting VIM resistance genes

bug

KS requests

Status: Open.

#180 In Clinical-Genomics/microSALT;

· samuell opened on Aug 21, 2024

Metrics file not output for case

bug

Status: Open.

#176 In Clinical-Genomics/microSALT;

· seallard opened on Jul 8, 2024

Switch CI from TravisCI to GitHub Actions

Effort L

Gain M

Status: Open.

#174 In Clinical-Genomics/microSALT;

· samuell opened on Jun 28, 2024

MicroSALT cannot start single sample case

bug

Status: Open.

#172 In Clinical-Genomics/microSALT;

· beatrizsavinhas opened on Feb 15, 2024

Slurm id file naming

Status: Open.

#170 In Clinical-Genomics/microSALT;

· seallard opened on Feb 5, 2024

Duplication rate missing in json output

bug

Status: Open.

#168 In Clinical-Genomics/microSALT;

· seallard opened on Jan 18, 2024

Jobs cannot be tracked for microsalt

bug

Status: Open.

#167 In Clinical-Genomics/microSALT;

· seallard opened on Jan 15, 2024

assembly issues in arcC loci for Staphylococcus Aureus

bug

Status: Open.

#164 In Clinical-Genomics/microSALT;

· talnor opened on Jan 8, 2024