https://github.com/catg-umag/ont-basecalling-demultiplexing - v2.5.1

Updates

• Dorado 1.0.2
• MultiQC 1.29

- Nextflow
Published by dialvarezs 12 months ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - 2.5.0

Changes:

Add parameter basecalled_input to allow already basecalled / demultiplexed data as input.

Updates:

Dorado 0.9.6

- Nextflow
Published by dialvarezs about 1 year ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - 2.4.2

Fixes: - Only trim adapters in basecalling process, preventing a bad generation of sequencing_summary.txt and further ToulligQC error.

Changes: - Increase default value of qscore_filter to 12.

Updates: - Dorado 0.9.5 - MultiQC 1.28

- Nextflow
Published by dialvarezs about 1 year ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - 2.4.1

Updates:

Dorado 0.9.1 MultiQC 1.27.1 NanoPlot 1.44.1

nf-schema plugin 2.3.0

- Nextflow
Published by dialvarezs over 1 year ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - 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+)

- Nextflow
Published by dialvarezs over 1 year ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - 2.3.1

Fixes: - Handle FastQC memory correctly - Handle ToulligQC title with spaces

Improvements: - Resource tweaking of FastQC, Nanoplot and ToulligQC

- Nextflow
Published by dialvarezs almost 2 years ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - 2.3.0

Improvements:

• Add nf-schema validation
• Remove parameters doradobasecallingextraconfig and doradodemuxextraconfig: the prefered now will be using ext.args, and the last one will
• Removed parameter skipdemultiplexing: now demultiplexing will be skipped if sampledata was not provided.
• Enable nextflow report by default

Fixes: - Barcodes were hardcoded in ToulligQC - ToulligQC thowed an error if experiment_name was not defined

- Nextflow
Published by dialvarezs almost 2 years ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - 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.

- Nextflow
Published by dialvarezs almost 2 years ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - v2.1.0

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

- Nextflow
Published by dialvarezs about 2 years ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - v2.0.0

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

- Nextflow
Published by dialvarezs over 2 years ago

https://github.com/catg-umag/ont-basecalling-demultiplexing - v1.0.0

Working version of the pipeline (before dropping Guppy support)

- Nextflow
Published by dialvarezs over 2 years ago