Merge pull request #719 from dufeiyu/update_germline

Update germline_detect_variants step

Merge pull request #589 from tmooney/set_default_memory_requirements

Set a default memory request for all tools.

Merge pull request #279 from jasonwalker80/add_process_inputs

Add process_inputs.pl to PP branch

Merge pull request #223 from dufeiyu/toil_compatibility

Add step to run add_bam_readcount_to_vcf_helper.py

Merge pull request #206 from dufeiyu/toil_compatibility

Add cle_annotated_vcf_filter step and strelka_cpu_reserved parameter

Merge pull request #203 from jasonwalker80/interleaved_fastq_pipe

DNA Alignment: Pipe Interleaved FASTQ