tempe_v1.2.2

Minor patch

Bugfixes:

• Set snpSniffer to default to false instead of true, this means that if all tasks are disabled or missing in the config we will only run the default alignment with bwa
• Fixed input/output for bcftools annotate - previously the annotation databases were considered as outputs, not inputs
• Shifted deepvariants dynamic memory allocation to be ~16G higher per bin, which is less prone to OOM kills in our testing
• Adjusted constitutional manta to place output files in the results_dir a bit earlier, which is better for downstream processing
• Added prepare_tumor_only resets to the tumor only variant callers that did not have this set already
• Omitting a denylist region within chunk4 of the calling intervals, this region is prone to significant walltime runouts #65
• Bumped to discordant_loci_extractor v0.1.6 to fix errors when input volume/data is low

Improvements:

• Configured tumor_only sigprofiler to use a more strictly filtered vcf, which yields comparable results to the somatic sigprofiler output
• Updated stats2lims to handle lane level stats #55

Full Changelog: v1.2.1...v1.2.2