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broadinstitute
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viral-classify
viral-ngs: taxonomic identification, classification, and filtering steps
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bump viral-core version 2.3.1 -> 2.3.3
#50
tomkinsc
closed
3 weeks ago
0
Edits to chunking blast function
#49
golu099
opened
3 months ago
0
update coveralls action; bump actions python to 3.10
#48
tomkinsc
closed
3 months ago
0
Changes made to chunking blast function
#47
golu099
closed
3 months ago
0
Adding arbitrary parameters to blastn_chunked_fasta function
#46
golu099
closed
5 months ago
0
Adding kraken output perl scripts
#45
golu099
closed
5 months ago
2
update viral-core 2.2.4 -> 2.3.1 (w/ python 3.8 -> 3.10)
#44
tomkinsc
closed
5 months ago
1
docker build fix and filter_taxids_to_focal_hits fix
#43
dpark01
closed
7 months ago
0
add metagenomics.taxlevel_plurality
#42
dpark01
closed
7 months ago
0
update docker base image to v2.2.3 of viral-core; Update conftest.py to account for breaking changes in the newer version of pytest
#41
tomkinsc
closed
10 months ago
0
change TravisCI badge to Actions badge in readme
#40
tomkinsc
closed
10 months ago
0
rename test action in CI
#39
tomkinsc
closed
11 months ago
0
update python modules evaluated for test coverage
#38
tomkinsc
closed
11 months ago
0
bump krona 2.7.1 -> 2.8.1
#37
tomkinsc
closed
11 months ago
1
Updating Docker with Lydia's Perl Scripts
#36
golu099
closed
10 months ago
4
expose more blast parameters on command line
#35
golu099
closed
5 months ago
0
add Lydia perl scripts to docker container
#34
golu099
closed
10 months ago
0
Expose kraken2 --minimum-hit-groups param
#33
tomkinsc
opened
1 year ago
0
bump diamond, kraken2, krona versions
#32
dpark01
closed
11 months ago
1
migration from Travis CI to GitHub Actions
#31
tomkinsc
closed
11 months ago
0
bump core
#30
dpark01
closed
3 years ago
0
bump viral-core to 2.1.16
#29
tomkinsc
closed
3 years ago
0
remove vestigial code path where revertBam was an optional param
#28
tomkinsc
closed
3 years ago
0
viral-core 2.1.10 -> 2.1.12 in Dockerfile
#27
tomkinsc
closed
3 years ago
0
remove usage of deprecated biopython IUPAC Alphabet
#26
tomkinsc
closed
3 years ago
0
update viral-core 2.1.8->2.1.10
#25
tomkinsc
closed
3 years ago
1
bump viral-core image 2.1.4 -> 2.1.8
#24
tomkinsc
closed
4 years ago
0
viral-core to 2.1.4
#23
dpark01
closed
4 years ago
0
kraken2 build fix for protein dbs
#22
dpark01
closed
1 year ago
0
kraken2 test coverage
#21
dpark01
closed
4 years ago
0
kraken build typo
#20
dpark01
closed
4 years ago
3
viral-core to 2.1.3
#19
dpark01
closed
4 years ago
0
viral-core 2.1.0 -> 2.1.1
#18
tomkinsc
closed
4 years ago
0
viral-core:2.0.21 - > 2.1.0
#17
tomkinsc
closed
4 years ago
0
filter bam from taxa
#16
dpark01
closed
4 years ago
0
kraken2
#15
dpark01
closed
4 years ago
2
dededuplicate
#14
dpark01
closed
4 years ago
0
viral-core to v2.0.21
#13
tomkinsc
closed
4 years ago
0
Restructure project towards a traditional python package
#12
yesimon
opened
4 years ago
4
krona tweaks
#11
dpark01
closed
4 years ago
0
krona fixes
#10
dpark01
closed
4 years ago
0
viral core 2.0.16 -> 2.0.18
#9
tomkinsc
closed
4 years ago
0
decouple read deduplication from taxonomic filtration
#8
dpark01
closed
4 years ago
1
bump docker base image; viral-core 2.0.15->2.0.16
#7
tomkinsc
closed
4 years ago
0
bump docker base image; viral-core 2.0.14->2.0.15
#6
tomkinsc
closed
4 years ago
0
deplete_bwa_bam removes all single-ended reads
#5
dpark01
closed
4 years ago
1
doc build and zstd updates
#4
dpark01
closed
4 years ago
0
add doc build
#3
dpark01
closed
4 years ago
0
add dust python command
#2
dpark01
closed
4 years ago
1
add krakenuniq summary report filter
#1
dpark01
opened
4 years ago
0
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