Cleanup of metrics preparation. Handle cases without merging of BAM prepped files. Do not do in-metrics de-duplication and use pysam to count duplicates. Use variant_regions for hybrid selection metrics if explicit bait/targets not specified
Finalize initial attempt at providing a template to multi-sample configuration bridge (#22). Fix GitHub retrieval, add fastq pairing, clean up input options and provide documentation.
Ensure closing of local file handles when setting up nested local loggers
Quiet variant filtration warnings on missing filter attributes since these fill up logs and make debugging difficult
Document the method for identifying Galaxy location files for finding genome indexes (#24).
allow fastq.gz and *.gz files in template creation.
adjust pairing to handle _R1, R2 file names. strip _R from description.
set aligner to false when using bams as input.
Merge pull request #25 from brentp/sample-config

WIP: allow fastq.gz and *.gz files in template creation.
Revert change to set aligner false for BAM files since BAM is commonly used to re-alignment from Illumina inputs
Provide template command to more easily prepare a local configuration template for customization. #22
Preserve YAML comments when downloading templates for local project preparation. Supplements #26
add comments to template for common options
Merge pull request #27 from brentp/template-comments

add comments to template for common options
Use Picards CollectInsertSizeMetrics to calculate the inner distance.
Add an attibute to run only the rnaseq-analysis.
Fall back to the original method of calculating the insert size for small files.
Generalize creation of population VCFs for separate from gemini requirement. Add all combined population VCFs to final upload directory. Thanks to @brentp
Provide initial check for improperly nested configuration variables in sample YAML file
Release v0.6.5