broadinstitute viral-phylo issues

broadinstitute / viral-phylo

viral-ngs: phylogenetics, annotation, intrahost variants

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Transition from samtools mpileup to bcftools mpileup in variant calling

#56 tomkinsc opened 5 months ago
0
update viral-core 2.1.20 -> 2.3.1 (w/ python 3.8 -> 3.10)

#55 tomkinsc closed 5 months ago
0
python open() now defaults to universal newlines; update mode'rU' -> 'r'

#54 tomkinsc closed 11 months ago
0
new method intrahost.merge_vcfs

#53 dpark01 opened 11 months ago
1
migrate from tbl2asn to table2asn

#52 tomkinsc opened 1 year ago
0
migration from Travis CI to GitHub Actions

#51 tomkinsc closed 5 months ago
0
bump mafft version 7.471 -> 7.508

#50 tomkinsc opened 1 year ago
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remove mummer wrapper and line from conda dependencies

#49 tomkinsc opened 1 year ago
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prep_genbank_files -- real sample ID names

#48 dpark01 closed 1 year ago
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prep_genbank -- real sample IDs

#47 dpark01 closed 1 year ago
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sanitize output tbl filename

#46 dpark01 closed 1 year ago
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fix typo

#45 dpark01 closed 1 year ago
0
small fixes

#44 dpark01 closed 1 year ago
0
small fixes/updates

#43 dpark01 closed 1 year ago
0
bump core

#42 dpark01 closed 3 years ago
0
bug fix note column

#41 dpark01 closed 3 years ago
0
purpose of sequencing

#40 dpark01 closed 3 years ago
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bump viral-core to 2.1.16

#39 tomkinsc closed 3 years ago
0
Revert "add derivedcols.py"

#38 dpark01 closed 3 years ago
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add derivedcols.py

#37 dpark01 closed 3 years ago
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add iso_dates option to biosample_to_genbank

#36 dpark01 closed 3 years ago
0
ncbi bugfixes

#35 dpark01 closed 3 years ago
0
ncbi file prep updates

#34 dpark01 closed 3 years ago
0
viral-core 2.1.10 -> 2.1.12 in Dockerfile

#33 tomkinsc closed 3 years ago
0
viral-core:2.1.9 -> viral-core:2.1.10

#32 tomkinsc closed 3 years ago
0
rollback viral-core to 2.1.9 for now

#31 tomkinsc closed 3 years ago
0
viral-core:2.1.9 -> viral-core:2.1.10

#30 tomkinsc closed 3 years ago
0
update viral-core 2.1.8->2.1.9

#29 tomkinsc closed 3 years ago
0
add alternative to V-Phaser2 for iSNV calling

#28 tomkinsc opened 4 years ago
0
vcf verbose output

#27 tomkinsc opened 4 years ago
2
bump viral-core image 2.1.4 -> 2.1.8

#26 tomkinsc closed 4 years ago
0
add bcftools to requirements

#25 tomkinsc closed 4 years ago
1
bump mafft version

#24 dpark01 closed 3 years ago
0
bump viral-core 2.1.4

#23 dpark01 closed 4 years ago
0
mafft 7.464 -> 7.467

#22 tomkinsc closed 4 years ago
0
add snp-sites tool

#21 dpark01 opened 4 years ago
0
add sequence cleanup and filtration functions

#20 tomkinsc opened 4 years ago
0
tbl2asn: remove old installer

#19 dpark01 closed 4 years ago
0
bump viral-core

#18 dpark01 closed 4 years ago
0
viral-core 2.1.0 -> 2.1.1

#17 tomkinsc closed 4 years ago
0
viral-core:2.0.21 - > 2.1.0

#16 tomkinsc closed 4 years ago
0
simplify fasta naming for one-chr genomes

#15 dpark01 closed 4 years ago
0
ncbi.biosample_to_genbank db_xref

#14 dpark01 closed 4 years ago
0
ncbi.biosample_to_genbank

#13 dpark01 closed 4 years ago
0
hotfix: tbl2asn conda version mismatch

#12 dpark01 closed 4 years ago
0
add optional mafft speed up for closely related genomes

#11 dpark01 opened 4 years ago
1
parameterize assembly method in prep_genbank_files

#10 dpark01 closed 4 years ago
0
add prep_genbank_files optional param to override assembly method

#9 dpark01 closed 4 years ago
0
mafft 7.402 -> 7.464

#8 tomkinsc closed 4 years ago
0
viral-core to v2.0.21

#7 tomkinsc closed 4 years ago
0