• Update the pipeline to nf-core 2.9.

• Add gnu/sort to sort annotation before uLTRA index

• Update citations

• Add background to pipeline png

• Update modules

  Tool	Previous version	New version
  isoseq3	3.8.1	3.8.2
  lima	2.6.0	2.7.1
  bamtools/convert	2.5.1	2.5.2
  gstama/merge	1.0.2	1.0.3
  uLTRA/index	0.0.4.2	0.1
  uLTRA/align	0.0.4.2	0.1
  samtools	1.17	1.17
  gnu/sort	----	8.25

Fixed

• Update minimap2 path test: Don’t set gtf option. It is not expected to be used with minimap2 is chosen.
• FIX: Don’t prepare gtf channel when minimap2 is chosen.

Fixed

• Fix pipeline image path
• params.input invalid type if pipeline is run with local file in samplesheet (was working with URL)

Added

• Fix issue #17. Thanks to Husen M. Umer.
• Zenodo DOI
• Update to template v2.7.2

Fixed

• Remove hard coded capped option for GSTAMA_FILELIST step. Now follow user choice. Thanks to Mazdak Salavati.

Dependencies

Update the pipeline to nf-core template v2.5.1. Update modules:

• samplesheet_check
• dumpsoftwareversion
• MultiQC

Fix aligner option documentation.

Pipeline performance improvement. When uLTRA path is selected, It reduce computation by indexing GTF once instead of chunk times.

nf-core/isoseq is a bioinformatics best-practice analysis pipeline for Isoseq gene annotation with uLTRA and TAMA. Starting from raw isoseq subreads, the pipeline:

• Generates the Circular Consensus Sequences (CSS)
• Clean and polish CCS to create Full Length Non Chimeric (FLNC) reads
• Maps FLNCs on the genome
• Define and clean gene models