v1.1.0

What's Changed

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

Changes to the core

• 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

Changes to existing Taskclasses:

• 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

New Task classes

• Add CorrectUmis to dagr tasks by @gpratt in #366

New Contributors

• @mjhipp made their first contribution in #357
• @jacarey made their first contribution in #380

Full Changelog: 1.0.0...1.1.0

Release 1.0.0

Release 1.0.0 is a major release with the following changes:

Major Changes

• Cross-building support moved from [2.11, 2.12] -> [2.12, 2.13]
• Significant extensions to the scatter/gather API to support grouping, sub-scattering etc.

Minor Changes

• Various new Tasks and updates to Task classes
• Pipe operators now support Option[Dependable]

Release 0.5.0

Release 0.5.0 is a minor release and includes the following changes:

• Attempt to alleviate scheduling bottleneck in dagr when there are lots of short running tasks (#332)
• Builds with scala 2.12.6 by default, and cross builds with 2.11.12 (was 2.11.11 by default and 2.12.2 otherwise) (#332)
• Reduce CPU requirement to 0.1 for trivial InJvm jobs (#332)
• Exposed the option to ignore unexpected barcodes in IlluminaBasecallsToSam
• Updated the readme with more documentation (#335)
• ErrorRateByReadPosition does pileups, which require memory linear to the depth. Usually it runs just fine in 4G, but in very deep data it will run out of memory. (#333)
• Added support for VarDict to call multiple alleles at the same site (#334)
• Propagate failures to parent tasks (tasks that created the failed task) (#329)

Release 0.4.0

This release is a minor release with some backwards compatibility breaks. Updates include:

• Minor updates to VarDictJava and VarDictJavaEndToEnd tasks.
• Fix to IlluminaBasecallsToSam task to correctly set MAX_READS_IN_RAM_PER_TILE
• Changes to fgbio tasks to work with fgbio 0.5.0
• Updated dependency versions

Release 0.3.0

Release 0.3.0 is a minor release and includes the following changes:

1. Several new Task classes for specific bioinformatics tools
2. Updates to existing Task classes
3. Upgrades to latest versions of several dependencies

Release 0.2.0

Release 0.2.0 includes the following changes:

• moved dagr.commons to https://github.com/fulcrumgenomics/commons
• moved dagr.sopt to https://github.com/fulcrumgenomics/sopt
• support for scala 2.12.2; we use this version by default.
• support for cross-building and publishing of scala 2.11.8 and 2.12.2
• added a task for the fgbio tool CollectDuplexSeqMetrics.

Release 0.1.3

Release 0.1.3 includes the following changes:

• Enabled cross building for scala 2.11 and 2.12
• Several updates to task classes for Picard and fgbio tasks
• Fix to JvmOutOfMemoryRetry so that it can find OOM tokens that are not whole lines
• Cleared up messages about why there are incomplete tasks at the end of a pipeline run
• Addition of task classes for Picard illumina basecalling related programs
• Added the ability for sopt to use classes with Companion.apply(String) as arguments
• Fix for how async io flags are propagated to picard Tasks

Release 0.1.2

Updated version to 0.12.