Release v1.0.1

Bump v1.0.1 – fixing conda recipe and CoPilote Agent Configuration (#…

Release v1.0.0

sr2silo can now be seamlessly integrated into workflows and V-Pipe, connecting to a Loculus instance for file sharing via pre-signed S3 links.

It manages environmental variables gracefully and installs via pip or conda.

What's Changed

• Separation of processing / submission CLI & Loculus File sharing for v0.2.0 by @gordonkoehn in #235

• Implement environment variable configuration with CLI parameter override by @gordonkoehn in #244

• build(deps): bump the pip group across 1 directory with 2 updates by @dependabot in #229

Full Changelog: v0.2.0...v1.0.0

Release v0.2.0

🚨 Breaking Changes

This release introduces a major restructuring of the CLI. The single command has been split into two separate commands:

• Separated CLI Commands (#215): Processing and submission are now independent operations
  • process-from-vpipe: Handles V-pipe output processing
  • submit-to-loculus: Manages submission to Silo (Loculus/S3)
  • Enables better workflow control and debugging
  • Allows resubmission without reprocessing
• Improvements
  • Fixed Snakemake logs on Euler (#216): Resolved logging issues in HPC environments
  • Cleaned up test data (#212): Improved test suite maintainability

Release v0.1.2

This release patches through changes in the transient dependency smallgenomeutilities. A new version of smallgenomeutilities changes the default behaviour of the paired_read_merge command. Unpaired reads are now by default keep and written to the same output file.This means sr2silo implements them, by default now. This vastly improved logs and error messages.

What's Changed

• Handeling unpaired genomic reads by @gordonkoehn in #209

Release v0.1.1

• fix: changed unknown char for amino acids in padding
• fix: multiple batch ids causing snakemake clash
• add version tracking to metadata
• adds option to skip the read pair merging
• updated various github actions
• starts with proper semantic versioning

Release v0.1.0

Release version 0.1.0

Release v0.0.4

Release v0.0.4

Paired-Read Merger and Validation

Implements the first entire pipeline, including the merging of paired-end reads.

We bring down the resource requirements for the amino acid alignment and formatting bugs on insertions.

• bug: on larger 700Mb bam files, the processing runs OOM at 16GB RAM #168
• Integrate Read Merging into Start-End Workflow #157
• Adding Read Pairing & Merge Functionality to sr2silo #158
• Add eq to AlignedReads and subclasses #148
• bug: positions zero or one based genspectrum/nextclade/pysam #161

And more are addressed.

Release 0.0.2

What's Changed

Initial Project Setup

New Contributors

• @dependabot
• @gordonkoehn

Full Changelog: https://github.com/cbg-ethz/sr2silo/commits/0.0.2