2.4.0

Updates:

• Dorado 0.9.0
• MultiQC 1.26
• Samtools 1.21
• nf-schema plugin 2.2.1

Improvements:

• Disabled demultiplexing during basecalling to avoid reprocessing the entire basecalling workflow in case of an incorrect kit specification
• Refactor pipeline to follow better conventions
• Format code according to Nextflow LSP
• Collect tool versions using eval and topics (preview feature Nextflow 24.04+)

2.3.1

Fixes:

• Handle FastQC memory correctly
• Handle ToulligQC title with spaces

Improvements:

• Resource tweaking of FastQC, Nanoplot and ToulligQC

2.3.0

Fixes:

• Barcodes were hardcoded in ToulligQC
• ToulligQC thowed an error if experiment_name was not defined

Improvements:

• Add nf-schema validation
• Remove parameters dorado_basecalling_extra_config and dorado_demux_extra_config. The prefered way now is to use ext.args.
• Removed parameter skip_demultiplexing: now demultiplexing will be skipped if sample_data was not provided.
• Enable nextflow report by default

2.2.0

• Added nanoq and toulligQC, and use them by default instead of NanoPlot and pycoQC.
• Added new parameter to choose which qc tools to run (of FastQC, NanoPlot, nanoq, pycoQC and toulligQC).
• Include a patched version of MultiQC to generate quality bar plots instead of line plots for nanoq.
• Simplify basecalling and demux and other pipeline improvements.
• Minor changes to MultiQC config.
• Update tool versions.

v2.1.0

• Update versions (Dorado, MultiQC, Samtools).
• Update Dorado default model
• Some code cleanup

v2.0.0

• Use Dorado (https://github.com/nanoporetech/dorado) as basecaller instead of Guppy.
• Some report improvements

v1.0.0

Working version of the pipeline (before dropping Guppy support)