Additional pipeline automation, including for Bayesian ID check

wtsi-npg / genotyping

Components of the WTSI genotype analysis pipeline.

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Closed iainrb closed 8 years ago

iainrb commented 8 years ago

New ready_workflow.pl script to:
- Query iRODS for multiple QC plex results and write as VCF
- Generate a pipeline analysis directory and appropriate YML config files
Remove genotyping_yml.pl; functionality is now part of ready_workflow.pl
Modify Perl QC scripts and Ruby workflows to support multiple VCF inputs with QC plex calls
Refactoring of run_qc.pl with improved documentation and handling of command-line arguments
Updated years in Genotyping/Version.pm to include 2016

iainrb commented 8 years ago

Fixes earlier issue with zcall_workflow.rb. Correctly checks that vcf and plex_manifest arrays are non-empty before doing Bayesian identity QC.