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BD2KGenomics
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toil-lib
A common library for functions and tools used in toil-based pipelines
Apache License 2.0
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Add Deca (resolves #108)
#109
fnothaft
opened
7 years ago
1
Add DECA method in toil_lib.tools.spark_tools
#108
fnothaft
closed
7 years ago
0
Add benchmarking mode (resolves #101)
#107
fnothaft
opened
7 years ago
0
Misc ADAM recompute upgrades (resolves #90)
#106
fnothaft
opened
7 years ago
1
Added bowtie2 and SNAP aligners (resolves #102)
#105
fnothaft
opened
7 years ago
0
Add sambamba index (resolves #103)
#104
fnothaft
closed
7 years ago
0
Add Sambama index
#103
fnothaft
closed
7 years ago
0
Add two new aligners
#102
fnothaft
opened
7 years ago
0
Add benchmarking mode to all tools
#101
fnothaft
opened
7 years ago
0
Make docker image parametrizable for all tools
#100
fnothaft
opened
7 years ago
0
Added variant callers for benchmarking (resolves #97)
#99
fnothaft
opened
7 years ago
3
Fix typo in samblaster parameter name
#98
fnothaft
closed
7 years ago
0
Add new variant callers to benchmark against
#97
fnothaft
opened
7 years ago
0
Added alternate sort and duplicate marking tools (resolves #95)
#96
fnothaft
closed
7 years ago
3
Add sambamba, samblaster
#95
fnothaft
closed
7 years ago
0
Instrument GATK functions (resolves #93)
#94
fnothaft
closed
7 years ago
3
Log timings to master for GATK pipeline
#93
fnothaft
closed
7 years ago
0
Add sort option to STAR (resolves #91)
#92
jvivian
closed
7 years ago
0
Add sort option to STAR
#91
jvivian
closed
7 years ago
0
ADAM recompute upgrades
#90
fnothaft
opened
7 years ago
0
Remove dockercall (resolves #68)
#89
fnothaft
closed
7 years ago
13
Add fusion output from Kallisto (resolves #87)
#88
jvivian
closed
7 years ago
1
Add fusion results to Kallisto output
#87
jvivian
closed
7 years ago
0
Revert "Within KeepPairs" to "Within" (resolves #85)
#86
jvivian
closed
7 years ago
1
Revert Within KeepPairs to Within in STAR
#85
jvivian
closed
7 years ago
0
Add splice junction from STAR to output (resolves #83)
#84
jvivian
closed
7 years ago
0
return rnaSJ.out.tab for STAR
#83
jvivian
closed
7 years ago
0
FileIOStore symlinks don't work with docker
#82
glennhickey
closed
7 years ago
1
S3IOStore cannot transfer big files
#81
glennhickey
closed
7 years ago
2
Support piped commands in docker_call
#80
glennhickey
closed
7 years ago
2
Move jpfeil/oncotator:1.9 to cgl-docker-lib
#79
jvivian
opened
7 years ago
0
Remove dockercall (resolves #68)
#78
jvivian
opened
7 years ago
16
Fix rsem_postprocess typo (resolves #76)
#77
jvivian
closed
7 years ago
1
Fix typo in rsem_postprocess
#76
jvivian
closed
7 years ago
0
Remove mutable=True (resolves #74)
#75
jvivian
closed
7 years ago
1
Remove mutable=True from toil-lib
#74
jvivian
closed
7 years ago
0
Release 1.1.2
#73
jvivian
closed
7 years ago
0
Refactor rsem postprocess (resolves #70, resolves #71)
#72
jvivian
closed
7 years ago
0
Refactor rsem_postprocess
#71
jvivian
closed
7 years ago
1
Update to quay.io tools in run_rsem_postprocess
#70
jvivian
closed
7 years ago
0
Add support for Redwood
#69
jvivian
opened
7 years ago
2
Remove docker_call
#68
jvivian
closed
7 years ago
3
1.1.1 Release
#67
jvivian
closed
7 years ago
0
Add --limitBAMsortRAM argument
#66
jvivian
closed
7 years ago
0
not pip-installable on cgcloud toil-box-templated toil-leader?
#65
ArtRand
closed
7 years ago
1
Make indel realignment optional (resolves #63)
#64
jpfeil
closed
7 years ago
2
Make indel realignment optional
#63
jpfeil
closed
7 years ago
0
Add mark secondary option to run_bwakit
#62
jpfeil
closed
7 years ago
3
Add mark secondary option to run_bwakit
#61
jpfeil
opened
7 years ago
0
Add documentation
#60
almussel
opened
7 years ago
1
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