fulcrumgenomics dagr issues

fulcrumgenomics / dagr

A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs

MIT License

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issues

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Fix bug in SortBam sort order option

#404 mjhipp closed 5 months ago
1
Add new options to ClipBam and CallDuplexConsensusReads

#403 mjhipp closed 5 months ago
1
Updated build and dependencies:

#402 tfenne closed 2 years ago
2
There may be a deadlock in the task scheduler that freezes or slows pipeline execution

#401 clintval opened 2 years ago
0
Remove the codacy badge

#400 nh13 closed 2 years ago
1
Bump com.fulcrumgenomics.commons version to 1.2.0

#399 mjhipp closed 3 years ago
3
Allow callers of Var2VcfValid to turn on printing of a variant's END tag

#398 clintval closed 3 years ago
2
Expose sort option in picard FastqToSam task

#397 mjhipp closed 3 years ago
1
Update unittests.yaml

#396 nh13 closed 3 years ago
1
Change CI from travis-ci to github actions

#395 nh13 closed 3 years ago
0
Update output file option in BwaMem task args

#394 mjhipp closed 3 years ago
0
Update travis badge

#393 jacarey closed 3 years ago
0
Jc allow memory override eib

#392 jacarey closed 3 years ago
0
update travis secure vars

#391 nh13 closed 3 years ago
0
Update travis to use bionic distribution, openjdk8

#390 mjhipp closed 3 years ago
0
Expose sorting option in IlluminaBasecallsToSam

#389 mjhipp closed 3 years ago
1
Add two new GroupReadsByUmi task options

#388 mjhipp closed 3 years ago
1
Expose -5 option for BwaMem task

#387 mjhipp closed 3 years ago
0
Round cores in log statements to 2 decimals of precision

#386 clintval closed 3 years ago
0
Always use the logical processor count for system max cores

#385 clintval closed 3 years ago
2
Yf contaminate and estimate bid

#384 yfarjoun opened 3 years ago
0
dagR back door analysis

#383 ghost closed 4 years ago
0
Back door paths analysis

#382 ghost closed 4 years ago
7
Expose `INCLUDE_SECONDARY_ALIGNMENTS` for MergeBamAlignment task.

#381 jacarey closed 4 years ago
1
Add flag to allow for the output of all alignments in bwa mem.

#380 jacarey closed 4 years ago
1
Bugfix/nested non unit tasks

#379 nh13 closed 4 years ago
1
Add VarDictJava's experimental --fisher option to VarDictJavaEndToEnd

#378 mjhipp closed 4 years ago
1
CPU and memory resource detection should be Docker container aware.

#377 jacarey opened 4 years ago
1
Add withPrefix and withSuffix to Pipeline

#376 mjhipp closed 4 years ago
1
Adding a pipeline to parse dagr execution reports.

#375 nh13 opened 4 years ago
0
ResourceSet bug when subsetting resources and some performance optimizations

#374 nh13 closed 4 years ago
0
Various Task Manage Speedups

#373 nh13 closed 4 years ago
1
Add the "-K" option from bwa

#372 nh13 closed 4 years ago
0
API should not allow mixins between VariableResources and FixedResources

#371 clintval opened 4 years ago
3
Why does Dagr use the physical processor count instead of logical for Macs only?

#370 clintval closed 3 years ago
1
Use Files.deleteIfExists() in `DeleteBam` rather than `paths.filter(F…

#369 tfenne closed 5 years ago
0
PicardTask to use the Intel inflater/deflater only if it is safe, by default

#368 clintval closed 4 years ago
5
PicardTask to allow overriding default use of JDK inflater

#367 clintval closed 5 years ago
2
Add CorrectUmis to dagr tasks

#366 gpratt closed 5 years ago
2
Attempt to make the GATK tasks a) auto-detect GATK version and b) swi…

#365 tfenne closed 5 years ago
4
Added deletion of CSI indices in DeleteBam.

#364 tfenne closed 5 years ago
1
Improve performance of flatMap in ScatterGather

#363 nh13 opened 5 years ago
0
Add Scatter.empty

#362 nh13 closed 5 years ago
2
Add a test for ScatterGather showing failed deferred access with map

#361 nh13 opened 5 years ago
0
Add support for empty tasks

#360 nh13 closed 5 years ago
2
Build a Scatter from a method that returns a sequence of results.

#359 nh13 closed 5 years ago
3
Scatter gather flatMap/groupBy fixup

#358 nh13 closed 5 years ago
1
Add Picard's BaitDesigner and ExtractSequences tasks

#357 mjhipp closed 5 years ago
3
Move cross-building to 2.12 and 2.13

#356 tfenne closed 5 years ago
1
Empty tasks

#355 nh13 opened 5 years ago
5