Version 4 Release Candidate 2

Second release candidate for version 4 of sunbeam, intended for internal testing. Major changes include:

• Revert host filtering to filtering mapped reads (new method is more direct but doesn't allow for filtering on certain parameters that are needed)

Additional minor fixes and updates

Version 4 Release Candidate 1

First release candidate for version 4 of sunbeam, intended for internal testing. Major changes include:

• Many components of sunbeam have been moved extensions to minimize installation and usage issues with the core pipeline, qc and decontam are the remaining core components
• Deprecated --cluster-config snakemake option replaced with profiles, also reduces sunbeam's command line interface by moving options to the profile
• Improved logging and reporting standards for sunbeam and extensions
• Restructured to snakemake standards for tarball installation methods
• Switch test suite from bash to pytest to increase ease and efficiency of testing
• Updated documentation

Minor changes:

• Fixed minor bugs in sunbeam config modify
• Added cutadapt options to sunbeam config
• Catch empty fastqc reports that would otherwise error out
• Replace os.system calls with subprocess
• Use unmapped reads directly from samtools instead of previous method of filtering them manually
• Remove rbt and biopython, rewriting functions manually instead of using heavy dependencies

Version 3.1.1

This is a minor bugfix release addressing the following:

• Upgrade manage-version.sh to work with any version (before or after 3.1) and always keep itself on the latest version
• Allow multiple targets with sunbeam run --target_list [TARGET, ...]

Version 3.1.0

Minor version release with some cluster bugs solved and the addition of a new script for managing different versions of sunbeam. Also fixing a build issue in docs and adding significant documentation around the software structure and usage options.

• Upgrade snakemake to v7.15.1, this fixed two issues with running jobs on the cluster
• Add manage-versions.sh which manages versions of sunbeam automatically for users in a single repo
• Fix build errors for previous versions of docs introduced when trying to add versioning info from sunbeamlib
• Improve the install script's decision making on when to use mamba vs conda and add informative errors
• Remove 'str' calls from snakemake that are no longer necessary (snakemake <5.7 requirement)
• Add 'Sunbeam Commands', 'Software Structure', 'install.sh', and 'manage-versions.sh' pages to docs

Version 3.0.1

This is a minor bugfix release addressing the following:

• Add biom-format to Kraken env
• Fix sunbeam init not picking up extension configs
• Fix multiqc naming issue that seemed to arise across different multiqc versions

Version 3.0.0

First release of sunbeam version 3! Feedback and ideas for version 4 are welcomed. Major upgrades include:

Refactoring of virtual environments to create multiple, smaller environments which can be automatically managed with snakemake's inline conda option. User experience will be very similar but this should dramatically reduce issues arising from dependency incompatabilities
New command sunbeam extend to automatically install Sunbeam extensions! Use like sunbeam extend https://github.com/sunbeam-labs/sbx_report
sunbeam init and sunbeam config update now add options for extensions you've installed to your default config file! (#247)
Change out blastx and blastp for diamond to dramatically increase speed

Other changes:

Support use of .smk file extensions in Sunbeam extensions (in addition to .rules)
Support mamba as an alternate package dependency solver at install time, for faster installs
Updated the path to the Illumina adapter sequences from hardcoded to templated (fixes #150 and #152)
Use the updated kraken2 classifier instead of kraken
Update other dependencies (trimmomatic -> 0.3.9; grabseqs -> 0.6.1; snakemake -> >5.7.0)
Include komplexity filtered reads in QC summary report (#252)
No longer double counts reads that map to multiple hosts causing negative non-host numbers (#304)

Version 3 Release Candidate 1

First release of sunbeam version 3, intended for internal testing over the next two weeks followed by a full release. Major upgrades include:

• Refactoring of virtual environments to create multiple, smaller environments which can be automatically managed with snakemake's inline conda option. User experience will be very similar but this should dramatically reduce issues arising from dependency incompatabilities
• New command sunbeam extend to automatically install Sunbeam extensions! Use like sunbeam extend https://github.com/sunbeam-labs/sbx_report
• sunbeam init and sunbeam config update now add options for extensions you've installed to your default config file! (#247)
• Change out blastx and blastp for diamond to dramatically increase speed

Other changes:

• Support use of .smk file extensions in Sunbeam extensions (in addition to .rules)
• Support mamba as an alternate package dependency solver at install time, for faster installs
• Updated the path to the Illumina adapter sequences from hardcoded to templated (fixes #150 and #152)
• Use the updated kraken2 classifier instead of kraken
• Update other dependencies (trimmomatic -> 0.3.9; grabseqs -> 0.6.1; snakemake -> >5.7.0)
• Include komplexity filtered reads in QC summary report (#252)
• No longer double counts reads that map to multiple hosts causing negative non-host numbers (#304)

Version 2.1.0

This pull request from release-2.1.0 to stable incorporates a number of fixes for recent issues:

• Updates to documentation (#169, #230, #231)
• Fix missing samtools (#224)
• Integration test updates to schedule weekly builds (#222)
• Fix issues with old paired-end illumina adapters (#221)
• Script updates to use conda commands instead of source commands (#220)
• Add h5py package explicitly to avoid dependency metadata problem (#219)
• Add multiQC to build QC report (#203)
• Use multithreading for cutadapt in QC (#202)
• Correct conda channel priority during install (#201)
• Update documentation to spell out requirements (#199)
• New megahit failure handling (#194)
• Enforce sample wildcard constraints in Snakemake rules (#190)
• Run megahit multithreaded (#189)

We also added a build manifest, which is run every time on integration testing to make it easier for users to install a working config from conda.

Version 2.0.2

This is a minor bugfix release to fix a recent problem with package dependencies (#225).

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)