Release v1.1.0 · fulcrumgenomics/dagr

What's Changed

This release upgrades many of dagr's dependencies to their latest versions, and removes scala 2.12 support.

Scatter gather flatMap/groupBy fixup by @nh13 in #358
Add support for empty tasks by @nh13 in #360
Add Scatter.empty by @nh13 in #362
Various Task Manage Speedups by @nh13 in #373
Add withPrefix and withSuffix to Pipeline by @mjhipp in #376
Bugfix/nested non unit tasks by @nh13 in #379
Always use the logical processor count for system max cores by @clintval in #385
Round cores in log statements to 2 decimals of precision by @clintval in #386

Added deletion of CSI indices in DeleteBam. by @tfenne in #364
Add Picard's BaitDesigner and ExtractSequences tasks by @mjhipp in #357
Attempt to make the GATK tasks a) auto-detect GATK version and b) swi… by @tfenne in #365
PicardTask to allow overriding default use of JDK inflater by @clintval in #367
Use Files.deleteIfExists() in DeleteBam rather than `paths.filter(F… by @tfenne in #369
Add the "-K" option from bwa by @nh13 in #372
PicardTask to use the Intel inflater/deflater only if it is safe, by default by @clintval in #368
Add VarDictJava's experimental --fisher option to VarDictJavaEndToEnd by @mjhipp in #378
Add flag to allow for the output of all alignments in bwa mem. by @jacarey in #380
Expose INCLUDE_SECONDARY_ALIGNMENTS for MergeBamAlignment task. by @jacarey in #381
Expose -5 option for BwaMem task by @mjhipp in #387
Add two new GroupReadsByUmi task options by @mjhipp in #388
Expose sorting option in IlluminaBasecallsToSam by @mjhipp in #389
Allow memory override for ExtractIlluminaBarcodes by @jacarey in #392
Update output file option in BwaMem task args by @mjhipp in #394
Expose sort option in picard FastqToSam task by @mjhipp in #397
Allow callers of Var2VcfValid to turn on printing of a variant's END tag by @clintval in #398

Full Changelog: 1.0.0...1.1.0