nf-core/scnanoseq: nf-core/scnanoseq v1.3.0 - Steel Elephant

v1.3.0 [2026-06-26]

Credits

Special thanks to a new contributor to scnanoseq:

• Nick Youngblut

Enhancements

• #94 Strict syntax conversion: converted entire workflow to strict syntax and reorganized into <name>/main.nf directory structure
• #93 and #55 Upgraded IsoQuant from v3.6.1 to v3.13.0 and removed chromosome-splitting logic in the IsoQuant subworkflow due to improvements in IsoQuant; IsoQuant now processes all chromosomes in a single invocation
• #65 and #61 Replaced NanoFilt with Chopper for read filtering, with gzip compression of intermediate split FASTQ files to reduce disk usage
• #87 Added --skip_blaze_demux parameter to allow skipping BLAZE demultiplexing
• Added SPLIT_SEQ module using seqkit for splitting FASTQ files, replacing the previous split approach
• Updated CAT_FASTQ to the nf-core module which now supports compressed inputs
• Moved gzip compression to pre-extraction step to minimize uncompressed FASTQ footprint in work directories
• Upgraded nf-core template from 3.2.1 to 3.5.1

Parameter changes

• --skip_fastqc default changed from false to true (disabled by default due to runtime issues with long-read data)
• --skip_fastq_nanocomp default changed from false to true
• --skip_bam_nanocomp default changed from false to true
• #99 --skip_toulligqc default changed from false to true
• --skip_blaze_demux added (default: true)

Fixes

• #83 Isoquant count matrix headers are now compatible with Seurat (removed leading # from header line). Note that lastest version of IsoQuant also resolves this issue.

Software dependencies

| Dependency | Old version | New version | | ---------- | ----------- | ----------- | | IsoQuant | 3.6.1 | 3.13.0 | | Chopper | - | 0.10.0 | | NanoFilt | 2.8.0 | removed |