v4.6.0

Notes

This PR updates the remove_low_complexity, filter_reads, and parse_fastq functions to (dramatically) improve memory efficiency.

What's Changed

• 485 fix filter reads and remove low complexity memory inefficiency by @Ulthran in #487

Full Changelog: v4.5.2...v4.6.0
sunbeamlabs/sunbeam: Python: Python 3.12.3, Snakemake: 8.10.8, Conda: conda 24.3.0
sunbeamlabs/sunbeam:slim: Python: Python 3.12.3, Snakemake: 8.10.8, Conda: conda 24.3.0
sunbeamlabs/cutadapt: Python: Python 3.12.3, Cutadapt Version: 4.8
sunbeamlabs/komplexity: Rustc: rustc 1.77.2 (25ef9e3d8 2024-04-09), Komplexity komplexity v0.3.5
sunbeamlabs/qc: Python: Python 3.12.0, Conda: conda 24.3.0, BWA: Version: 0.7.18-r1243-dirty, FastQC: FastQC v0.12.1, Trimmomatic: 0.39
sunbeamlabs/reports: Python: Python 3.12.3, Numpy Version: 1.26.4, Pandas Version: 2.2.2

v4.5.2

What's Changed

• 460 fix docker tagging by @Ulthran in #461
• Treat blanks as empty strings by @Ulthran in #465
• Pass SUNBEAM_VER from workflow to Dockerfiles by @Ulthran in #470
• Include docker image reports (mostly package versions) in releases by @Ulthran in #471
• 4.5.2 Release by @Ulthran in #480

Full Changelog: v4.5.1...v4.5.2

sunbeamlabs/sunbeam: Python: Python 3.12.2, Snakemake: 8.10.4, Conda: conda 24.1.2
sunbeamlabs/sunbeam:slim: Python: Python 3.12.2, Snakemake: 8.10.4, Conda: conda 24.1.2
sunbeamlabs/cutadapt: Python: Python 3.12.2, Cutadapt Version: 4.7
sunbeamlabs/komplexity: Rustc: rustc 1.77.1 (7cf61ebde 2024-03-27), Komplexity komplexity v0.3.5
sunbeamlabs/qc: Python: Python 3.12.0, Conda: conda 24.1.2, BWA: Version: 0.7.17-r1188, FastQC: FastQC v0.12.1, Trimmomatic: 0.39
sunbeamlabs/reports: Python: Python 3.12.2, Numpy Version: 1.26.4, Pandas Version: 2.2.1

v4.5.1

API Addition

• --docker_tag is now an option for sunbeam run

What's Changed

• 455 restructure containerization by @Ulthran in #456
• Remove slurm log naming hack by @Ulthran in #458

Full Changelog: v4.4.0...v4.5.1

v4.5.0

What's Changed

• 455 restructure containerization by @Ulthran in #456
• Remove slurm log naming hack by @Ulthran in #458

Full Changelog: v4.4.0...v4.5.0

v4.4.0

What's Changed

• Fix install.sh by @Ulthran in #452
• Use hack to create slurm_extra resource within each rule by @Ulthran in #454

Full Changelog: v4.3.7...v4.4.0

v4.3.7

What's Changed

• Dynamic resource allocation by @Ulthran in #400
• Include and exclude options for sunbeam run by @Ulthran in #445
• Upgrade snakemake to v8 by @Ulthran in #441
• 359 containerize internal envs by @Ulthran in #447
• Refactor CI/CD workflows by @Ulthran in #449

Full Changelog: v4.2.0...v4.3.7

Version 4.2.0

What's Changed

• Improve benchmarking reports by @Ulthran in #422
• Allow cutadapt opts to be empty by @Ulthran in #428
• Update qc.py for filter komplexity id bug by @naomiwilson in #430
• Fix remove_low_complexity logic by @Ulthran in #436
• Add spaced-name test data and associated e2e test by @Ulthran in #435
• Fix snakemake to 7.32 by @Ulthran in #438

New Contributors

• @naomiwilson made their first contribution in #430

Full Changelog: v4.1.0...v4.2.0

Version 4.1.0

What's Changed

• Use main and remove master, stable, and dev by @Ulthran in #407
• Rework configuration to not use deprecated mechanisms by @Ulthran in #412
• Add clean_decontam target by @Ulthran in #408
• Remove annoyances by @Ulthran in #414
• Replace setup.py with pyproject.toml by @Ulthran in #416
• Prep v4.1.0 release by @Ulthran in #419

Full Changelog: v4.0.0...v4.1.0

Version 4

Release of Sunbeam version 4! This version includes the outsourcing of many non-essential parts of the pipeline to optional extensions, integration of snakemake profiles to simplify the command line and make interactions with various cluster/cloud management systems easier, a new and improved testing suite (written with PyTest), and various bug fixes and QoL improvements.

• 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
• 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
• Improving filter_reads efficiency on large hostid sets and catching errors in sequence header matching

Version 4 Release Candidate 3

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

• Improving filter_reads efficiency on large hostid sets and catching errors in sequence header matching