Enhancements

• (https://github.com/nf-core/scnanoseq/issues/44) All output files produced by isoquant are now produced in the results file
• (https://github.com/nf-core/scnanoseq/issues/47) BLAZE scripts has been removed from the repo so the actual published code can be used
• (https://github.com/nf-core/scnanoseq/issues/47) Added new whitelists for 10X 3v4 and 10X 5v3
• Upgraded nf-core template to 3.2.1
• Upgraded nanocomp nf-core module (no version change)
• Seurat process now places the seurat object to pipeline outputs
• Updated metro diagram

Fixes

• (https://github.com/nf-core/scnanoseq/issues/45) Reference files are now accepted in .zip format
• (https://github.com/nf-core/scnanoseq/issues/56) Fixed an error where using --skip_dedup would end the pipeline early
• (https://github.com/nf-core/scnanoseq/issues/58) Fixed UMI length for 5 prime chemistries
• Fixed an error caused by --skip_qc and --skip_seurat
• No longer output uncorrected correct barcodes
• Fixed issue with linting.yml preventing automatic template PRs

Software dependencies

Enhancements

• Inputs for IsoQuant are split on chromosome to allow for faster processing
• The read counts QC metric is now able to leverage NanoPlot counts if FastQC is skipped
• Added oarfish as an option for quantification
• Added picard markdupes as an option for deduplication

Fixes

• The ‘Post Trim Read QC’ and ‘Post Extract Read QC’ nodes on the metro diagram have been placed in correct locations (closes issue #36)
• The BLAZE process in the example config has been corrected to use cpus instead of --threads

Software dependencies

v1.0.0 [2024-10-07]

Initial release of nf-core/scnanoseq, created with the nf-core template.