Merge branch 'release/0.178' into develop
in post_process(), only change group if we created the file, and permsissions if files were not already world readable
Use /software/vertres/lib/R-2.15.2/ as PluriTest does not work with R version 3
Use /software/vertres/lib/R-2.15.2/ as PluriTest does not work with R version 3
latest bcftools has changed the -o option to -O
genome_studio_import_from_irods pipeline replaced with genome_studio_import_from_irods_and_convert_to_vcf pipeline featuring new illumina_coreexome_manifest_to_map step and updated genome_studio_fcr_to_vcf step that both use fcr-to-vcf
genome_studio_import_from_irods pipeline replaced with genome_studio_import_from_irods_and_convert_to_vcf pipeline featuring new illumina_coreexome_manifest_to_map step and updated genome_studio_fcr_to_vcf step that both use fcr-to-vcf
moved penncnv tests to the the genome_studio_import_and_genotype_comparison.t script
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into develop
replaced hard-coded local paths with env vars
added support for arbitrary filetypes
arbitrary filetypes limited to 4 chars long, and test added to Manager.t to ensure they can be used in steps
added a search_by_metadata() method
altered sequenom_csv_to_vcf step to take sequenom_plex_storage_dir and reference name and get plex manifest from irods
new add_metadata_from_warehouse option to get public_name, and irods_path is also stored as metadata
irods->get_file(dest_file) changed to (dest) for consistency and use by irods_get_files_by_basename step when the irods_path is known
new vcf_sample_from_metadata option to allow public_name meta value to be put in output vcf
use sample metadata as the default vcf_sample_from_metadata option value in sequenom_csv_to_vcf step
add/override sample_cohort in irods metadata with donor_id from warehouse, in case irods info is missing
version bump