Releases: cfe-lab/MiCall
HIVdb 9.4
Stitched consensus
The main changes were:
- Added a stitched consensus #745
- Updated to HIVdb 9.0 #686
- Noncoding regions #589
- Launch proviral pipeline #706
- Added chimeric Ghana references for HIVGHA project code #806
- Added concordance evaluation #821
For the full list of issues, see the milestone.
Note: v7.15.12 is only a change to the MiCall watcher to suspend the proviral upload into QAI, as it is currently failing.
v7.15.13 pins merge-mates to the commit that I used to test v7.15 (there have since been new commits that break our code)
To do when putting the new release in place:
- Add Charlotte to email recipients
- Add a new sample to the list of samples to test: 90906A-HCV_S122 from run 16-Oct-2020.M01841
Primers by project
SARS-CoV-2 support
De novo assembly
The big change is #442, adding a de novo assembly method to the standard remapping method.
Also included:
- #486 a project region for GP120, and report V3LOOP coverage with G2P alignments while GP120 reports coverage from remapped or assembled reads.
- #524 Insertion counts are wrong.
- #471 and #473 improve efficiency of micall_watcher script.
See the milestone for a complete list.
De novo assembly (preview)
Development preview of #442 de novo assembly.
HCV subtype bug
Container Runs
The main improvements in this release are in the MiCall watcher, specifically changing to Kive's new container runs (#460). Related fixes are #458 and #459.
- Update HIVdb to 8.8 (#448).
- Some bugs when combining MIDI and whole genome samples: #469, #468, #465, #463, #462, #454, and #450.
For the complete list of issues, see the milestone.
Configuration changes:
- Convert old Kive runs to container runs.
- Upload pipeline definitions to QAI for #441.
- Remove bowtie2 from Kive's host system, because it interferes with the version inside the Singularity container.
- Update kiveapi to 0.12.
HCV Reports
Add HCV reports (#412), then update HCV resistance rules (#436).
- Combine whole-genome and MidHCV samples to get complete coverage in HCV reports (#427 and #438).
- Fix a couple of bugs in the consensus sequences (#417 and #420).
- Add more details to resistance results (#445).
- Fix external datasets (#452).
- Error handling in micall_watcher (#449, #451, and #453).
For the full list of changes, see the milestone.