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CCBR
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XAVIER
An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
https://ccbr.github.io/XAVIER/
MIT License
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chore: run pre-commit on all files
#78
kelly-sovacool
closed
9 months ago
0
fix spelling errors
#76
kelly-sovacool
closed
9 months ago
1
Print helpful message when xavier CLI is called with no arguments
#75
kelly-sovacool
closed
9 months ago
0
update citation file with Zenodo DOI after we cut the next release
#74
kelly-sovacool
closed
4 months ago
1
ci: update Python version for mkdocs
#73
kopardev
closed
9 months ago
1
`xavier` with no argument gives error
#72
kopardev
closed
9 months ago
0
Version not printed "correctly" on headnode
#71
kopardev
opened
10 months ago
2
fix: final somatic merge
#70
dnousome
closed
10 months ago
1
Somatic callers not merging correctly
#69
dnousome
closed
10 months ago
0
docs: create CITATION.cff
#68
kelly-sovacool
closed
10 months ago
1
chore: update pre-commit & prettier config from our template
#67
kelly-sovacool
closed
10 months ago
0
fix: add rerun incomplete and fix bed
#66
dnousome
closed
10 months ago
1
ci: delete sync-fork action
#65
kelly-sovacool
closed
10 months ago
0
Fix requirements.txt
#64
kopardev
closed
9 months ago
0
document the release process
#63
kelly-sovacool
closed
10 months ago
0
docs: update changelog/docs
#62
dnousome
closed
11 months ago
0
fix: add additional IUPAC
#61
dnousome
closed
11 months ago
0
fix: varscan iupac
#60
dnousome
closed
11 months ago
0
fix: mm10 kraken2 location
#59
dnousome
closed
11 months ago
0
Hotfix for mm10 Kraken
#58
dnousome
closed
11 months ago
0
Docs update
#57
dnousome
closed
1 year ago
0
Hotfix- somatic merge rules and bugs in hostname
#55
dnousome
closed
1 year ago
0
QC Fix
#54
dnousome
closed
1 year ago
1
Documentation Update
#53
dnousome
closed
1 year ago
2
XAVIER 3.0 Biowulf
#52
dnousome
closed
1 year ago
1
ci: github assignee is used by default for auto-add-user-project
#51
kelly-sovacool
closed
1 year ago
0
fix: if else error
#50
dnousome
closed
1 year ago
0
Updates/bug fixes/new version v3.0
#49
kopardev
closed
1 year ago
0
ci: fix fork-sync action for NCIPangea
#48
kelly-sovacool
closed
1 year ago
0
Clean up failing "fork sync" actions
#47
kelly-sovacool
closed
1 year ago
0
Fix GH action for NCIPangea forked version
#46
kopardev
closed
1 year ago
2
cleanup PIPELINES_HOME on FRCE
#45
kopardev
opened
1 year ago
0
fix(spooker): typo in 'which' command
#44
kelly-sovacool
closed
1 year ago
1
Frce test
#43
samarth8392
closed
1 year ago
0
Specify threads/cpus in cluster config
#42
kelly-sovacool
opened
1 year ago
0
KeyError in somatic variant calling rules in FRCE
#41
samarth8392
closed
1 year ago
3
Biowulf resources location changed
#40
dnousome
closed
1 year ago
3
Hotfix: set tmp dir dynamically
#39
kelly-sovacool
closed
1 year ago
2
Set tmp disk dynamically
#38
kelly-sovacool
closed
1 year ago
0
Don't overwrite user's config files unless runmode == 'init'
#37
kelly-sovacool
closed
1 year ago
0
On hotfix: add pre-commit config to enforce conventional commits style
#36
kelly-sovacool
closed
1 year ago
1
Add pre-commit config to enforce conventional commits style
#35
kelly-sovacool
closed
1 year ago
0
Error pulling docker images on FRCE
#34
samarth8392
closed
1 year ago
5
Fix gzip check in rule `ffpefilter_mafs`
#33
kelly-sovacool
closed
1 year ago
1
Temporary disk path assumes mode=slurm, fails on local mode
#32
kelly-sovacool
closed
1 year ago
5
Error running XAVIER on frce
#31
samarth8392
closed
1 year ago
2
Support custom genomes
#30
kelly-sovacool
opened
1 year ago
0
Allow users to override config template
#29
kelly-sovacool
closed
1 year ago
1
Gracefully handle when no reads map to a chromosome
#28
kelly-sovacool
opened
1 year ago
0
Subset small test dataset
#27
kelly-sovacool
closed
3 months ago
6
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