nf-core/scnanoseq
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
10xgenomicslong-read-sequencingnanoporescrna-seqsingle-cell
Version history
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_dedupwould 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_qcand--skip_seurat - No longer output uncorrected correct barcodes
- Fixed issue with linting.yml preventing automatic template PRs
Software dependencies
| Dependency | Old version | New version |
|---|---|---|
BLAZE | 2.2.0 | 2.5.1 |
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
oarfishas an option for quantification - Added
picard markdupesas 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
| Dependency | Old version | New version |
|---|---|---|
IsoQuant | 3.5.0 | 3.6.1 |
MultiQC | 1.25 | 1.25.1 |
v1.0.0 [2024-10-07]
Initial release of nf-core/scnanoseq, created with the nf-core template.
subscribers
47
stars
38
open issues
8
open PRs
2
last release
3 days ago
last update
3 days ago
