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fulcrumgenomics
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dagr
A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs
MIT License
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New Tasks
#354
averagehat
opened
5 years ago
1
Add new options to CallDuplexConsensusReads
#353
nh13
closed
5 years ago
1
Adding Scatter/Gather methods flatten and flatMap, Gather method scatter, and some bug fixes
#352
nh13
closed
5 years ago
2
Implement helper method PicardTask.withValidationStringency()
#351
clintval
closed
5 years ago
1
Add a global configuration option to control when to fall back to system
#350
nh13
opened
5 years ago
0
Move to mill
#349
nh13
opened
5 years ago
0
Optionally check configureExecutable config value path actually exists
#348
clintval
closed
3 years ago
7
Allow building a Core resource from String
#347
clintval
closed
5 years ago
2
Add the Picard task AddOrReplaceReadGroups
#346
clintval
closed
5 years ago
1
Handle the VarDictJava exception when no read groups or sample names are present
#345
clintval
closed
5 years ago
1
Add Picard BuildBamIndex to dagr tasks
#344
clintval
closed
5 years ago
3
trimming status of input fastqs for FastqToBam
#343
basesLoaded
opened
5 years ago
0
Adding the groupBy method to scatter/gathering
#342
nh13
closed
5 years ago
2
Add Picard VcfFormatConverter task
#341
clintval
closed
5 years ago
3
add an optional ploidy argument to the HaplotypeCaller
#340
evanmauceli
closed
5 years ago
2
First tile and tile limit exposed in IlluminaBasecallsToSam (debug)
#339
clintval
closed
5 years ago
1
Add tumor-normal calling mode to VarDictJavaEndToEnd
#338
clintval
closed
5 years ago
5
Create Var2VcfValid task and expose options in VarDictJavaEndToEnd
#337
clintval
closed
5 years ago
2
Allow optional piped tasks
#336
nh13
closed
5 years ago
1
Updated the readme with more documentation.
#335
tfenne
closed
6 years ago
2
Added support for VarDict to call multiple alleles at the same site
#334
gpratt
closed
6 years ago
1
ErrorRateByReadPosition does pileups, which require memory linear to …
#333
tfenne
closed
6 years ago
1
Two small-ish changes to try and make pipelines go a little faster
#332
tfenne
closed
6 years ago
1
Updated build to latest sbt, added git-hashes to snapshots and update…
#331
tfenne
closed
6 years ago
1
Update to work with fgbio-0.5.0
#330
nh13
closed
6 years ago
2
Propagate failures to parent tasks (tasks that created the failed task)
#329
nh13
closed
6 years ago
1
Add modifyPipeline hook.
#328
jacarey
closed
6 years ago
2
DO NOT MERGE: This was my take on adding a hook to transform the pipe…
#327
jacarey
closed
6 years ago
1
DO NOT MERGE: Expose a way to modify the pipeline prior to execution.
#326
nh13
closed
6 years ago
1
Remove version eye badge and update doc version
#325
nh13
closed
6 years ago
1
MAX_READS_IN_RAM_PER_TILE was not being set
#324
nh13
closed
6 years ago
1
TaskManager states cores used as a fraction with floating point error
#323
clintval
closed
3 years ago
0
Missing spaces in the printed command line arguments
#322
nh13
closed
6 years ago
1
Release 0.3.0 PR
#321
tfenne
closed
6 years ago
0
Bumped the commons and sopt dependencies to latest release versions.
#320
tfenne
closed
6 years ago
1
Clip Bam updates
#319
nh13
closed
6 years ago
1
Updates to VarDictJava and VarDictJavaEndToEnd
#318
nh13
closed
6 years ago
3
I want to know all the inputs and outputs produced by the pipeline, and who made them
#317
nh13
opened
6 years ago
0
Removing project-specific build files.
#316
nh13
closed
6 years ago
0
add CollectHsMetrics argument for option to output PER_BASE_COVERAGE …
#315
maxmaliska
closed
6 years ago
2
Exposed fgbio options --async-io, --compression, --tmp-dir, and --log…
#314
nh13
closed
7 years ago
2
Exposed fgbio options --async-io, --compression, and --tmp-dir
#313
nh13
closed
7 years ago
1
New task for SortBam.
#312
tfenne
closed
7 years ago
3
Add a few more options to consensus calling tasks
#311
nh13
closed
7 years ago
1
Add the clip overlapping reads option to the ClipBam task
#310
nh13
closed
7 years ago
1
Added task for ClipBam in fgbio with all flag options available
#309
maxmaliska
closed
7 years ago
4
Added task for fgbio's FastqToBam.
#308
tfenne
closed
7 years ago
1
Make Configuration thread-safe.
#307
nh13
closed
7 years ago
1
Dagr overhaul v1
#306
nh13
opened
7 years ago
2
WIP: Dagr Dashboard
#305
nh13
opened
7 years ago
0
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