Release Release v0.2.6 · maize-genetics/seq_sim

What's New

See individual changes below.

Replaced all ProcessRunner.runCommand("./gradlew", "run", ...) calls with direct Clikt command parsing via CommandName().parse(args). This eliminates the overhead of spawning new Gradle/JVM processes for each pipeline step.
Added restoreOrchestratorLogging() to maintain proper log file separation after each step runs.
All paths are now resolved to absolute, normalized paths for consistency. This prevents issues with relative path resolution when working directories change.
Changed config section parsing from map?.let { ... } to if (configMap.containsKey(...)) pattern. This allows pipeline steps to run with defaults even when config section is empty/null (i.e., just specifying the key enables the step).
Added missing parameter features in downsample_gvcf and covert_to_fasta steps.
General "QoL" updates to example pipeline YAML file.

Fixed biokotlin-tools gzip naming (biokotlin-tools automatically compresses output and adds .gz extension)
Temporary directories are now always cleaned up if they exist, not just when files were actively used from them.
Added cleanup of ALL existing file appenders when setting up a new log file
Prevents log bleeding where messages from step $N + 1$ appear in step $N$'s log file
Properly stops old appenders before removing them
Corrected binary name issue where "biokotlin" was called instead of "biokotlin-tools"

Download the appropriate archive for your system:

# Extract the archive
tar -xf seq_sim-v0.2.6.tar
# or
unzip seq_sim-v0.2.6.zip

# Run the application
./seq_sim-v0.2.6/bin/seq_sim --help

Full Changelog: v0.2.5...v0.2.6