v2.1.0

What's Changed

• Release v2.1.0 by @leahkemp in #24

Full Changelog: v2.0.0...v2.1.0

Notable changes

• Add rule and sample info to slurm log files
• Get naming convention of log output dir consistent
• Add pipeline tests
• Speedups
• Allow dynamic inclusion of recal resources - also stop need for user to manually write the flags
• Simplify code
• Functionize code
• Improve documentation
• Fix fastqc/multiqc error
• Fix file path that makes download from google cloud bucket not work
• Discourage using home dir in docs
• Clarify output files
• Remove g.vcf that causes error in vcf_annotation_pipeline

v2.0.0

What's Changed

• Dev by @leahkemp in #23

Full Changelog: v1.0.1...v2.0.0

Notable changes

• Improve log outputs (file naming and location written)
• Some speedups to GPU accelerated runs
• Add minimal testing dataset
• Allow RECALIBRATION: RESOURCES: in the configuration file to take a dynamic number of files and remove the need for the user to write the flag prefix (breaking change)
• Better practice code
• Improve documentation
• Fix code for downloading GATK resource bundle from google cloud bucket

Patch_1

Patch to fix error that pops up for rule "gatk_Apply_BQSR" associated with the java memory allocation for this rule.

First release!

Make gatk conda env compatible with parabricks gatk version

As it stands, this causes an error at gatk_GenotypeGVCFs for cohort runs