T1k HLA Genotyping

T1k HLA Genotyping

This release adds HLA Genotyping to both the BWA-GATK and Sentieon Alignment workflows. The process is done using the T1k software. For more information, see our readme: https://github.com/kids-first/kf-alignment-workflow/blob/master/docs/T1K_README.md

Other Changes

• BWA-GATK pipeline can now be run using CWLtool
• Optimized bamtofastq resource requests and stacking for CAVATICA
• Removed unnecessary bam merging step from Sentieon pipeline
• Sentieon BWA chunk size now matches BWA-GATK's
• Bug fixes, documentation cleanup, public app formatting

What's Changed

• 🐛 sentieon alignment cleanup by @dmiller15 in #131
• 🐛 alignment workflow cwltool compatibility by @dmiller15 in #135
• 🐛 enforce array length by @dmiller15 in #136
• 🐎 open bam processing resource ins by @dmiller15 in #137
• 🎉 add t1k to alignment by @dmiller15 in #138
• 📚 update reference names and links by @dmiller15 in #141
• 🔖 bump to release 2.11.0 by @dmiller15 in #142

Full Changelog: v2.10.0...v2.11.0