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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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Reduce data footprint post run
#128
samarth8392
opened
2 weeks ago
0
Clean up unused containers
#127
kelly-sovacool
closed
2 weeks ago
0
chore: 🤖 prepare release v3.1.2
#126
github-actions[bot]
closed
2 weeks ago
0
clean up unused containers
#125
kelly-sovacool
closed
2 weeks ago
0
fix: correct xavier base path for cache subcommand
#124
kelly-sovacool
closed
2 weeks ago
0
fix: upgrade multiqc docker with PYTHONPATH unset
#123
kelly-sovacool
closed
2 weeks ago
2
Error in MultiQC rule
#122
samarth8392
closed
2 weeks ago
0
Hotfix: Bug in assess_signficance.R script
#121
samarth8392
closed
1 month ago
0
Error in rule freec_exome_somatic
#120
samarth8392
closed
1 month ago
0
chore: 🤖 prepare release v3.1.1
#119
github-actions[bot]
closed
1 month ago
0
Fix docker tag name
#118
samarth8392
closed
1 month ago
0
fix: update multiqc docker to 1.15
#117
kelly-sovacool
closed
1 month ago
0
Update wes_base docker to v1.1.0
#116
samarth8392
closed
1 month ago
0
ci: set up action to build docker images automagically
#115
kelly-sovacool
closed
1 month ago
0
add debug subcommand for devs
#114
kelly-sovacool
closed
2 months ago
0
chore: 🤖 prepare release v3.1.0
#113
github-actions[bot]
closed
2 months ago
0
chore: specify ccbr_tools version v0.1.0
#112
kelly-sovacool
closed
2 months ago
0
refactor: update bin/redirect from RENEE
#111
kelly-sovacool
closed
3 months ago
0
fix: use spooker available in ccbrpipeliner module
#110
kelly-sovacool
closed
3 months ago
1
Bug fix related to correct default targets file in GUI
#109
samarth8392
closed
3 months ago
3
bug: Default targets file is always for hg38 when running GUI
#108
samarth8392
closed
3 months ago
0
Uploaded new test dataset for github workflow
#107
samarth8392
closed
3 months ago
13
deprecation warning - invalid escape sequence
#106
kelly-sovacool
opened
3 months ago
0
Use shared helper functions from ccbr_tools
#105
kelly-sovacool
closed
3 months ago
3
fix: increase mem for some rules; gatk contamination not run as localrule
#104
samarth8392
closed
3 months ago
1
merge default `--target` feature
#103
samarth8392
closed
3 months ago
0
Set default exome targets file based on genome
#102
kelly-sovacool
closed
3 months ago
0
get refactor gui changes into this branch
#101
samarth8392
closed
3 months ago
0
set default targets file based on genome if `--targets` not provided
#100
kelly-sovacool
closed
3 months ago
0
Refactor the XAVIER GUI
#99
kelly-sovacool
closed
3 months ago
1
refactor genome config structure to match RENEE
#98
kelly-sovacool
closed
3 months ago
0
Refactor as a python package
#97
kelly-sovacool
closed
3 months ago
0
Docs site versions
#96
kelly-sovacool
closed
3 months ago
5
show multiple versions on the docs website
#95
kelly-sovacool
closed
3 months ago
0
docs: Removed betterem extension from mkdocs.yml to improve rendering
#94
samarth8392
closed
3 months ago
0
MKdocs fails to render XAVIER title correctly
#93
samarth8392
closed
3 months ago
0
docs: rename GUI doc header in mkdocs.yml
#92
kelly-sovacool
closed
4 months ago
0
document the GUI
#91
kelly-sovacool
closed
4 months ago
2
Update GATK module on docker
#90
samarth8392
closed
1 month ago
0
Local rule: insufficient memory for the Java Runtime Environment
#89
samarth8392
closed
3 months ago
0
docs: add Zenodo doi
#88
kelly-sovacool
closed
4 months ago
0
Prepare to release v3.0.3
#87
kelly-sovacool
closed
4 months ago
1
fix: fixed issue #85
#86
samarth8392
closed
6 months ago
0
HPC/Biowulf memory overallocation
#85
samarth8392
closed
6 months ago
0
Fix varscan
#84
dnousome
closed
7 months ago
0
Varscan VCF rename
#83
dnousome
closed
7 months ago
1
add test dataset for mouse genome
#82
kelly-sovacool
closed
3 months ago
3
refactor xavier GUI
#81
kelly-sovacool
closed
3 months ago
0
refactor: update bin/redirect from RENEE
#80
kelly-sovacool
closed
9 months ago
0
numerous jobs failing with v3.0.2
#79
kelly-sovacool
closed
9 months ago
4
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