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cfe-lab
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MiCall
Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
https://cfe-lab.github.io/MiCall
GNU Affero General Public License v3.0
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Bump python-levenshtein from 0.21.1 to 0.25.0
#1052
dependabot[bot]
closed
8 months ago
1
Bump github-pages and jekyll in /docs
#1051
dependabot[bot]
closed
8 months ago
1
Bump nokogiri from 1.14.3 to 1.16.2 in /docs
#1050
dependabot[bot]
closed
8 months ago
10
Bump numpy from 1.24.3 to 1.26.4
#1049
dependabot[bot]
closed
5 months ago
1
Bump cutadapt from 3.7 to 4.6
#1048
dependabot[bot]
closed
8 months ago
1
Bump scipy from 1.10.1 to 1.12.0
#1047
dependabot[bot]
closed
8 months ago
3
Bump pytz from 2023.3 to 2024.1
#1046
dependabot[bot]
closed
8 months ago
5
Bump activesupport from 7.0.4.3 to 7.1.3.2 in /docs
#1045
dependabot[bot]
closed
8 months ago
1
Bump coverage from 7.2.7 to 7.4.3
#1044
dependabot[bot]
closed
8 months ago
3
Bump pandas from 2.0.2 to 2.2.1
#1043
dependabot[bot]
closed
7 months ago
3
Bump pytest from 7.4.0 to 8.1.1
#1042
dependabot[bot]
closed
8 months ago
1
Run apt-update on CI
#1041
Donaim
closed
8 months ago
0
Bump the ubuntu version
#1040
Donaim
closed
8 months ago
1
Fix singularity arguments
#1039
Donaim
closed
8 months ago
1
Use Ruff linter for the whole project
#1038
Donaim
closed
9 months ago
2
Add flake8 support
#1037
Donaim
closed
9 months ago
2
Feature Proposal: a Merger Tool
#1036
Donaim
opened
9 months ago
1
Mypy Integration and Type Annotations Enhancement
#1035
Donaim
closed
8 months ago
1
Mention devcontainers in CONTRIBUTING.md
#1034
Donaim
closed
1 year ago
1
Multiple python interpreters in dev container cause issues
#1033
Donaim
closed
1 month ago
5
Reimplement stitching algorithm
#1032
Donaim
closed
8 months ago
1
Complete CIGAR string definition
#1031
Donaim
closed
1 year ago
0
Reimplement the stitcher
#1030
Donaim
closed
8 months ago
6
Bump pandas from 2.0.2 to 2.1.2
#1029
dependabot[bot]
closed
8 months ago
2
Bump pytest from 7.4.0 to 7.4.3
#1028
dependabot[bot]
closed
8 months ago
5
Update minimap version
#1027
Donaim
closed
1 month ago
1
Implement sample merging
#1026
Donaim
opened
1 year ago
1
Bump numpy from 1.24.3 to 1.26.1
#1025
dependabot[bot]
closed
8 months ago
2
Aligning to defective start codon in `vpu`
#1024
Donaim
opened
1 year ago
0
Add aln2counts_simplify tool
#1023
Donaim
closed
1 year ago
3
Bump cutadapt from 3.7 to 4.5
#1022
dependabot[bot]
closed
8 months ago
3
Bump coverage from 7.2.7 to 7.3.2
#1021
dependabot[bot]
closed
8 months ago
3
Bump scipy from 1.10.1 to 1.11.3
#1020
dependabot[bot]
closed
8 months ago
2
Bump pandas from 2.0.2 to 2.1.1
#1019
dependabot[bot]
closed
1 year ago
1
Switch to Debian in Singularity image
#1018
Donaim
closed
8 months ago
1
Bump numpy from 1.24.3 to 1.26.0
#1017
dependabot[bot]
closed
1 year ago
1
Visualize stitched consensus
#1016
donkirkby
closed
8 months ago
2
Merge Haploflow into master
#1015
Donaim
opened
1 year ago
0
docs: describe genome.pos field of nuc.csv output
#1014
Donaim
closed
1 year ago
1
add HIV-AD option to utils/primer_locations script
#1013
Donaim
closed
1 year ago
1
Bump pytest from 7.4.0 to 7.4.2
#1012
dependabot[bot]
closed
1 year ago
2
Bump coverage from 7.2.7 to 7.3.1
#1011
dependabot[bot]
closed
1 year ago
1
Bump pytz from 2023.3 to 2023.3.post1
#1010
dependabot[bot]
closed
8 months ago
3
Bump pytest from 7.4.0 to 7.4.1
#1009
dependabot[bot]
closed
1 year ago
2
fix big deletion test for minimap
#1008
Donaim
closed
1 year ago
1
Bump pandas from 2.0.2 to 2.1.0
#1007
dependabot[bot]
closed
1 year ago
1
Make samplesheet parser tolerable to underscores in enum names
#1006
Donaim
closed
1 year ago
3
Correctly handle underscores in sample sheet parsing
#1005
Donaim
closed
4 months ago
1
Bump activesupport from 7.0.4.3 to 7.0.7.2 in /docs
#1004
dependabot[bot]
closed
8 months ago
3
Bump scipy from 1.10.1 to 1.11.2
#1003
dependabot[bot]
closed
1 year ago
1
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