- Fastqs with identical names (but which are in different subdirectories) are now able to be processed. The annotated CSVs are now stored in subdirectories which reflect the FASTQ structure.
- Gzipped FASTQ files can now be used. They must have the filename extension
.fastq.gz - We now provide a
--coresargument to Snakemake, allowing snakemake v5.11 and higher to be used - We provide better information about samples for which no reads are yet available (i.e. no FASTQ has been written)
Fixed dockerfile
Added dockerfile and github action to automatically build and push images from main to dockerhub on release
- Guppy-demuxed FASTQs can now be used. If this is the case, then
porechopis no longer a requirement for RAMPART to run. - Memory footprint has been drastically reduced. Testing with 1 million SARS-CoV-2 reads results in only ~20Mb for the server and ~10Mb for the client. This has necessitated the removal of filtering & the ability to change barcode-sample names via the UI. We hope to bring back this functionality in a future release.
- Improved installation documentation
- Fastqs can now be in nested folders (currently 2 levels are allowed)
- Light and Dark themes are now available and may be changed via a toggle in the header.
- We now display the version number in the footer to help with bug reports & debugging.