The make it stable release.

Since the previous release we have tidied up the report process, fixed a number of bugs around reading files aligned to hg38 including alts and made a few additional fixes.

From this point forwards we will be maintaining the main branch and all releases will have been tested on a selection of samples.

We have also established a dev branch which will contain new features currently under testing. Unless developing

As with all releases this code is for research use only.

The next release will focus on performance optimisations.

This code and the data contained within it are intended for research use only and should not be used for direct diagnostic purposes. The methylation-based classification and other analyses provided here may be considered by neuropathologists as supplementary information in the context of comprehensive diagnostic assessment, which should include clinical history, radiological findings, and complete histopathological and molecular evaluation. The final interpretation and diagnosis should always be made by qualified healthcare professionals based on all available information.

The authors of this software note that:
Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.

Using this software in any context, research or otherwise, is at the users own responsibility.

What's Changed

• Fix to browse local files by @mattloose in #57
• Fix/mobiledesign by @mattloose in #60
• Prevent dictionary error and require 3 or more reads for detecting a … by @mattloose in #63
• Fix/issue62 by @mattloose in #64
• Fix/reporting multi chrom by @mattloose in #65
• Fix/darkmode by @mattloose in #66
• Fixes minimum scale for cnv difference plot. by @mattloose in #67
• Fix to handle case differences in specfic file names. Resolves #70 by @mattloose in #71
• Issues/issue70 by @mattloose in #73
• Issues/fix fusion reporting by @mattloose in #74
• Minor change to spacing. by @mattloose in #75
• Moving around the MGMT results and providing a summary at the end of … by @mattloose in #76
• feat(sturgeon): add version-aware modkit command selection by @mattloose in #79
• feat: Add rsync support to BAM file detection by @mattloose in #80
• feat: adding templating for issues by @mattloose in #81
• Add rsync compatability by @mattloose in #83
• Create validate-branches.yml by @mattloose in #84
• Update validate-branches.yml by @mattloose in #88
• Update validate-branches.yml by @mattloose in #89
• Create auto-summarize-commits.yml by @mattloose in #90
• fix: correct sample ID handling with force_sampleid option by @mattloose in #96

Full Changelog: v0.1.0...v0.1.7

Robin Release

This is the intial release of our ROBIN tool as described in

ROBIN: A unified nanopore-based sequencing assay integrating real-time, intraoperative methylome classification and next-day comprehensive molecular brain tumour profiling for ultra-rapid tumour diagnostics
Simon Deacon, Inswasti Cahyani, Nadine Holmes, Graeme Fox, Rory Munro, Satrio Wibowo, Thomas Murray, Hannah Mason, Mark Housley, Daniel Martin, Abid Sharif, Areeba Patel, Robert Goldspring, Sebastian Brandner, Felix Sahm, Stuart Smith, Simon Paine, and Matthew Loose
doi:10.1101/2024.09.10.24313398
http://medrxiv.org/cgi/content/abstract/2024.09.10.24313398v1

Software is provided as is.

Please report any issues via github issues. We will also be monitoring the discussions forums for general advice. Documentation above and beyond the README file will be coming shortly.

Pull requests are welcome.

preview release

This is a test release for an initial build of ROBIN.

What's Changed

• Localfilepicker by @mattloose in #1
• Nano dx inprogress by @mattloose in #4
• Switching back to table for target coverage and implementing switchab… by @mattloose in #5
• Clair3 cnv mod by @mattloose in #6
• Feature/split UI proc by @mattloose in #14
• Feature/savestructure by @mattloose in #16
• Feature/betterfusionplots by @mattloose in #17
• adding netwrokx by @mattloose in #18
• Fix/fusiondetection by @mattloose in #19
• Fix/playbacksort by @mattloose in #20
• Refactoring reporting by @mattloose in #21
• Fixing logging to single log set up. by @mattloose in #22
• Fix/rstuff by @mattloose in #24
• SNP Call Docker Pull by @mattloose in #25
• Update/reporting by @mattloose in #28

New Contributors

• @mattloose made their first contribution in #1

Full Changelog: https://github.com/LooseLab/ROBIN/commits/v0.0.6