v5.0.1

Patches to the v5 release workflows and minor bug fixes.

Full Changelog: v5.0.0...v5.0.1

v5.0.0.c

Full Changelog: v5.0.0.b...v5.0.0.c

v5.0.0.b

Full Changelog: v5.0.0.a...v5.0.0.b

v5.0.0.a

Full Changelog: v5.0.0...v5.0.0.a

v5.0.0

Sunbeam is now pip/conda installable! We've restructured the entire pipeline inside of a Python library so that it is much easier to install and develop with. Many of the internals have also been refactored into cleaner classes (SampleList, SunbeamConfig, SunbeamProfile) and the documentation has received an overhaul (more automated sections so that it's easier to maintain). This release SHOULD retain backwards compatibility with all extensions but if you run into issues please report them so we can get fixes out.

What's Changed

• Restructure for pip/conda installation by @Ulthran in #501

Full Changelog: v4.7.0...v5.0.0

v4.7.0

What's Changed

• Update README.md by @naomiwilson in #491
• Add universal extension path function to sunbeamlib by @Ulthran in #496
• Check for adapter template by @Ulthran in #494
• Remove env pins and update docs by @Ulthran in #498
• 462 make updates to work with storage plugins by @Ulthran in #463

Full Changelog: v4.6.0...v4.7.0
sunbeamlabs/sunbeam: Python: Python 3.12.5, Snakemake: 8.18.0, Conda: conda 24.3.0
sunbeamlabs/sunbeam:slim: Python: Python 3.12.5, Snakemake: 8.18.0, Conda: conda 24.3.0
sunbeamlabs/cutadapt: Python: Python 3.12.5, Cutadapt Version: 4.9
sunbeamlabs/komplexity: Rustc: rustc 1.80.1 (3f5fd8dd4 2024-08-06), 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 3.12.5, Numpy Version: 2.0.1, Pandas Version: 2.2.2

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