Version 2.0.1

This is a minor bugfix release for a few version issues with dependencies.

• Incremented Snakemake version requirement for compatibility with recent conda (snakemake=5.5.0, #204/#215)
• Specified earlier megahit version to ensure compatbility with existing assembly behavior (megahit < 1.2, #216)
• Added integration test improvements (#211)

Version 2.0.0

This release introduces the ability to use an SRA number to start projects with sunbeam init, which should be a huge gain for reproducibility. We've also made a significant number of bug fixes and optimizations and improved the documentation around making extensions.

Major contributors:

• @louiejtaylor
• @ressy
• @zhaoc1
• @kylebittinger

v1.3.0 - Bugfixes

• Pinned dependencies for trimmomatic (0.36) and bwa (0.7.17)
• Better handling of empty values for host genomes and mapping target genomes
• More robust project folder creation in sunbeam init

Bugfixes

Better handling of sample name edge cases when guessing sample name format.

Bugfixes

Bugfixes in this release:

• Better sample name guessing (#139)
• Snakemake dependency locked to 4.8.1
• reports.rules refactored to avoid 'report' keyword
• no label truncation in vsearch

Low complexity read removal; assorted fixes

Changes:

• Komplexity now removes low-complexity reads by default instead of masking them.
• Better single-end rule behavior
• Documentation updates
• Various other bug fixes

Bugfixes and report format changes

• report outputs number of removed reads for each host after decontam
• use static binary for komplexity filtering to fix reliance on glibc
• remove max length for contigs (was 50k)

Version 1.0.0 (Stable)

First stable release.

Major changes from the pre-release version:

• Support for single-end sequencing reads
• Low-complexity masking using Komplexity
• Support for extensions
• Ergonomic command-line interface (via sunbeam command)
• Documentation on ReadTheDocs
• Better assembler
• Better ORF finder
• Arbitrary host/contaminant genome filtering
• Semantic versioning and updating
• Robust install and test scripts

Bugfixes

This update fixes numerous bugs.

Initial version

NOTE: This release is in alpha stage and any pipeline endpoints, config file parameters, and other major features may change at any time.

Initial release.