v1.3.4

easy-deploy: improvements to EC2 deployment (region flexibility, 8GB->300GB storage)
CondaPackage: faster verification of already installed packages
Various testing improvements including test timing and output capture

v1.3.3

Bugfixes with multi-segment genomes where the reference sequence names are not in alpha order. Improvements to lastal taxon filter default parameters based on optimization experiments with a broader range of diverse viruses.

v1.3.2

CondaPackage: conda packages now auto-update if the version number changes in the viral-ngs wrapper
SampleSheet: improved sanitization of sample sheet fields

v1.3.1

Illumina demux: sanitize SampleSheet sample names if necessary.

v1.3.0

Rewrite of scaffolding step (after de novo assembly and before read alignment based refinement). Remove VFAT (and Mosaik) and replace with a MUMmer based scaffolding routine.

v1.2.4

Bugfixes and unit testing of Trinity and fixes to Broad-specific pipeline scripts.

v1.2.3

easy_deploy now uses conda-based install, trinity install method now checks for meryl, tool wrappers for diamond and kraken check for prior existence, and diamond build has been changed from cmake to make for greater portability

v1.2.2

bam files are now sorted prior to running vphaser if they are passed in unsorted

v1.2.1

tool wrappers now fall back to our custom install methods if Python fails to decode the json response issued by conda; better logging for such cases.

v1.2.0

Move software dependencies to bioconda for greater reliability / cross-platform compatibility. Code fixes and stylistic cleanups. Migrate snakemake config file from JSON to YAML to allow for in-line documentation and comments. Initial work on metagenomic tools. Improvements to easy deploy.