* Added: gatk4/leftalignandtrimvariants
Additions:
- GATK4/LeftAlignAndTrimVariants module
- Use sars-ncov2 test data as this normalises a larger INDEL correctly.
Fixes#1801
* fixup: Added index to output spec
* fixup: Pattern of tbi output corrected to 'tbi'
* gatk4/leftalignandtrimvariants: Added intervals
Changes:
- gatk4/leftalignandtrimvariants now supports optional interval as BED
file
- Tests added with and without interval. Not test BED file excludes all
variants so no variants are actually normalised.
Fixes#1801
* fixup: leftalignandtrimvariants vcf->tbi fix
* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
