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IKIM-Essen
/
uncovar
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
https://ikim-essen.github.io/uncovar
BSD 2-Clause "Simplified" License
20
stars
6
forks
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feat: Update README.md for dark/light theme
#614
alethomas
closed
9 months ago
0
fix: QA genome generation
#613
alethomas
closed
9 months ago
0
feat: amplicon utils
#612
alethomas
opened
9 months ago
0
build: update Pangolin to 4.3
#611
github-actions[bot]
closed
9 months ago
0
build: update pangolin to version 4.3
#610
alethomas
closed
9 months ago
0
fix: more meaningful info for patient overview table
#609
alethomas
closed
9 months ago
0
Fix: change information for samples not accepted by QA in overview table
#608
alethomas
closed
10 months ago
0
fix: update multiqc
#607
alethomas
closed
10 months ago
0
Add rules for generating report only with qc measures
#606
alethomas
opened
10 months ago
0
chore(deps): bump docker/setup-buildx-action from 2 to 3
#605
dependabot[bot]
closed
10 months ago
0
chore(deps): bump docker/setup-qemu-action from 2 to 3
#604
dependabot[bot]
closed
9 months ago
0
chore(deps): bump alstr/todo-to-issue-action from 4.6 to 4.11
#603
dependabot[bot]
closed
9 months ago
0
chore(deps): bump actions/checkout from 2 to 4
#602
dependabot[bot]
closed
9 months ago
0
chore(deps): bump docker/login-action from 2 to 3
#601
dependabot[bot]
closed
9 months ago
0
chore(deps): bump snakemake/snakemake-github-action from 1.24.0 to 1.25.1
#600
dependabot[bot]
closed
9 months ago
0
chore(deps): bump docker/build-push-action from 3 to 5
#599
dependabot[bot]
closed
9 months ago
0
fix: switch from jupyter notebook to script
#598
alethomas
closed
11 months ago
0
fix: constrain nbformat version, trying to ensure notebook compatibility
#597
johanneskoester
closed
10 months ago
1
perf: update to varlociraptor 8.4
#596
johanneskoester
closed
9 months ago
0
feat: ignore the timestamp on the human genome reference file
#595
Kallepan
closed
1 year ago
0
build: update Pangolin to 4.3
#594
github-actions[bot]
closed
10 months ago
0
chore(deps): bump github/super-linter from 4.10.1 to 5.0.0
#593
dependabot[bot]
closed
10 months ago
0
chore(deps): bump peter-evans/create-pull-request from 4 to 5
#592
dependabot[bot]
closed
9 months ago
0
fix: replace ragoo with ragtag
#591
vBassewitz
opened
1 year ago
0
fix: changes in path requirements for snakedeploy
#590
AKBrueggemann
closed
1 year ago
4
feat: add additional primer file for ont
#589
alethomas
closed
4 months ago
1
chore: temporarily disable pre-commit ci action as it currently fails during installation (waiting for new release)
#588
johanneskoester
closed
1 year ago
0
fix: use homopolymer-pair-HMM-mode of Varlociraptor in case of nanopore reads
#587
johanneskoester
closed
11 months ago
0
chore(master): release 0.16.0
#586
github-actions[bot]
closed
9 months ago
1
fix: improved clonality event definition, usage of major subclone for assembly polishing; upgrade to varlociraptor 6.0
#585
johanneskoester
closed
1 year ago
0
fix: pre-commit action
#584
alethomas
closed
4 months ago
0
fix: ont vc failing
#583
alethomas
closed
9 months ago
0
build: update Pangolin to 4.2
#582
github-actions[bot]
closed
10 months ago
0
chore(deps): bump alstr/todo-to-issue-action from 4.6 to 4.10
#581
dependabot[bot]
closed
10 months ago
1
chore(deps): bump khan/pull-request-workflow-cancel from 1.0.0 to 1.0.1
#580
dependabot[bot]
closed
9 months ago
0
chore(deps): bump docker/build-push-action from 3 to 4
#579
dependabot[bot]
closed
10 months ago
1
refactor: work around bug in snakefmt that adds two lines after each include by moving an if statement into common.smk
#578
johanneskoester
closed
1 year ago
0
chore(deps): bump github/super-linter from 4.9.7 to 4.10.1
#577
dependabot[bot]
closed
1 year ago
0
chore(deps): bump github/super-linter from 4.9.7 to 4.10.0
#576
dependabot[bot]
closed
1 year ago
1
fix: use latest varlociraptor release and ignore all biases in case of known lineage variant calling
#575
johanneskoester
closed
1 year ago
0
fix: kraken db
#574
alethomas
closed
1 year ago
0
chore(deps): bump alstr/todo-to-issue-action from 4.6 to 4.9
#573
dependabot[bot]
closed
1 year ago
1
feat: Coar implementation
#572
ka-block
closed
4 months ago
2
chore(deps): bump alstr/todo-to-issue-action from 4.6 to 4.8
#571
dependabot[bot]
closed
1 year ago
1
-Oz generates a .vcf.gz!!
#570
github-actions[bot]
opened
1 year ago
0
remove once pangolin 4.1.3 is available in bioconda
#569
github-actions[bot]
closed
10 months ago
0
build: update Pangolin to 4.1.3
#568
github-actions[bot]
closed
1 year ago
1
chore(deps): bump amannn/action-semantic-pull-request from 4 to 5
#567
dependabot[bot]
closed
1 year ago
1
chore(deps): bump actions/checkout from 2 to 3.1.0
#566
dependabot[bot]
closed
1 year ago
1
chore(deps): bump github/super-linter from 4.9.6 to 4.9.7
#565
dependabot[bot]
closed
1 year ago
0
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