mbhall88/tbpore issues and pull requests

#58 - chore(main): release 0.7.1

Pull Request - State: closed - Opened by github-actions[bot] 6 months ago - 1 comment
Labels: autorelease: tagged

#57 - fix: update rasusa usage for latest version

Pull Request - State: closed - Opened by mbhall88 6 months ago - 1 comment

#56 - TBpore fails while running rasusa

Issue - State: closed - Opened by ycode-sh 6 months ago - 8 comments

#55 - chore(main): release 0.7.1

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment
Labels: autorelease: pending

#54 - chore(main): release 0.7.0

Pull Request - State: closed - Opened by github-actions[bot] about 1 year ago - 1 comment
Labels: autorelease: tagged

#53 - Expose subsampling options

Issue - State: closed - Opened by mbhall88 about 1 year ago - 1 comment

#52 - Add option for strongly connected components

Issue - State: closed - Opened by mbhall88 about 1 year ago - 1 comment

#51 - Add mapping reads stats

Pull Request - State: closed - Opened by mbhall88 almost 2 years ago

#50 - Add stats

Pull Request - State: closed - Opened by mbhall88 almost 2 years ago

#49 - Subsampled meaning

Issue - State: closed - Opened by jloubser almost 2 years ago - 3 comments

#48 - Sort fastq to ensure reproducibility

Issue - State: closed - Opened by mbhall88 almost 2 years ago

#47 - Better handling of decontamination database

Issue - State: closed - Opened by mbhall88 almost 2 years ago - 1 comment

#46 - Remove only fastq extension

Pull Request - State: closed - Opened by mbhall88 about 2 years ago - 1 comment

#45 - Error calling samtools (return code 1)

Issue - State: closed - Opened by FlorianePoint about 2 years ago - 4 comments

#44 - Add cache directory option

Pull Request - State: closed - Opened by mbhall88 about 2 years ago - 1 comment

#43 - Singularity Container read-only file system error

Issue - State: closed - Opened by pedrodcb about 2 years ago - 6 comments

#42 - Add option to set decontamination database index path

Pull Request - State: closed - Opened by mbhall88 about 2 years ago - 3 comments

#41 - Update README to refer to the decontamination index from figshare and other README updates

Pull Request - State: closed - Opened by leoisl over 2 years ago - 3 comments

#40 - Comparing paper results with results with new filters (min_depth 5, min_qual 25, min_mq 30)

Issue - State: closed - Opened by leoisl over 2 years ago - 14 comments

#39 - add release workflow

Pull Request - State: closed - Opened by mbhall88 over 2 years ago - 1 comment

#38 - Investigate `just test-run` not working

Issue - State: closed - Opened by leoisl over 2 years ago - 7 comments

#37 - Run several samples at once

Issue - State: closed - Opened by leoisl over 2 years ago - 4 comments

#36 - Build a tree from clustering

Issue - State: closed - Opened by leoisl over 2 years ago - 12 comments

#35 - Make the reference configurable

Issue - State: open - Opened by leoisl over 2 years ago - 10 comments

#34 - Switch away from conda

Issue - State: closed - Opened by leoisl over 2 years ago - 15 comments

#33 - Move decontamination DB index to zenodo

Issue - State: closed - Opened by leoisl over 2 years ago

#32 - Add conda recipe and release v0.1.0

Issue - State: closed - Opened by leoisl over 2 years ago

#31 - Test the impact on clustering of changing `minimap2` index to use less RAM

Issue - State: open - Opened by leoisl over 2 years ago - 3 comments

#30 - Improve README.md

Pull Request - State: closed - Opened by leoisl over 2 years ago - 1 comment

#29 - Adds subcommand `tbpore cluster`

Pull Request - State: closed - Opened by leoisl over 2 years ago - 2 comments

#28 - Add flag to make decontamination optional?

Issue - State: closed - Opened by leoisl over 2 years ago - 2 comments

#27 - Check md5sum or sha256 of decontamination DB index to ensure we have the correct index

Issue - State: closed - Opened by leoisl over 2 years ago - 3 comments

#26 - Adding decontamination and a few other misc stuff

Pull Request - State: closed - Opened by leoisl over 2 years ago - 1 comment

#25 - Create subcommand `tbpore cluster`

Issue - State: closed - Opened by leoisl over 2 years ago - 15 comments

#24 - Add minimap2 index URL

Issue - State: closed - Opened by leoisl over 2 years ago

#23 - Comparing `H2H` and `tbpore` output step by step

Issue - State: closed - Opened by leoisl over 2 years ago - 7 comments

#22 - Threshold for the phred-scaled VCF call quality

Issue - State: closed - Opened by leoisl over 2 years ago - 19 comments

#21 - Remove contamination

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment

#20 - Decontamination has a huge effect on real data tests

Issue - State: closed - Opened by leoisl over 2 years ago - 27 comments

#19 - Performance

Issue - State: closed - Opened by leoisl over 2 years ago - 4 comments

#18 - Duplicated files input bug

Issue - State: closed - Opened by leoisl over 2 years ago

#17 - Directory input bug

Issue - State: closed - Opened by leoisl over 2 years ago - 2 comments

#16 - Real data test, tbpore vs head-to-head pipeline

Issue - State: closed - Opened by leoisl over 2 years ago - 66 comments

#15 - Check H37RV data

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment

#14 - Add sample example

Issue - State: closed - Opened by leoisl over 2 years ago - 4 comments

#13 - Update README.md

Issue - State: closed - Opened by leoisl over 2 years ago

#12 - Cryptic Mac OS CI issue

Issue - State: closed - Opened by leoisl over 2 years ago - 4 comments

#11 - Linting

Issue - State: closed - Opened by leoisl over 2 years ago - 1 comment

#10 - Output directory param or output consensus param?

Issue - State: closed - Opened by leoisl over 2 years ago - 5 comments

#9 - Cache mykrobe/ctx binary skeletons

Issue - State: closed - Opened by leoisl over 2 years ago - 2 comments

#8 - tbpore, version 0.1.0

Pull Request - State: closed - Opened by leoisl over 2 years ago - 10 comments

GitHub / mbhall88/tbpore issues and pull requests