nf-core/isoseq v2.0.0 - Sapphire Duck [05/09/2024]

• New entrypoint option to skip isoseq pre-processing.
• Update the pipeline to nf-core 2.14.1.
• Update modules.
• nf-validation version pinned PR25
• Upgrade from isoseq3 to isoseq (version 4) Fix segmentation fault PR27
• Add alternative entrypoint PR10

Added

• A new entreypoint system has been implemented to allow the user where to start the analysis.
• The isoseq entrypoint runs the full pipeline.
• The map entrypoint runs the pipeline from the mapping step.
• This new entreypoint option make possible to use the isoseq pipeline for analysis PacBio data when subreads are not provided, or for users who want to benefit from the mapping + TAMA analysis for their Nanopore data.

Fixed

• Update modules to their nf-test version (bamtools/convert, custom/dumpsoftwareversions, gnu/sort, gstama/collapse/ gstama/merge, gstama/polyacleanup, gunzip, isoseq/refine, lima, minimap2/align, pbccs,ultra/align, ultra/index)

• Since isoseq3 switch to version 4, it has been rename isoseq

  Tool	Previous version	New version
  bamtools/convert	2.5.2	2.5.2
  isoseq	3.8.2	4.0.0
  lima	2.7.1	2.9.0
  minimap2/align	2.24	2.28
  gnu/sort	8.25	9.3
  multiqc	1.21	1.24.1

nf-core/isoseq v1.1.5 - Byzantium Buzzard [02/08/2023]

• 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

nf-core/isoseq v1.1.4 - Teal Albatross [13/03/2023]

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.

nf-core/isoseq v1.1.3 - Blue Grouse [06/03/2023]

Fixed

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

nf-core/isoseq v1.1.2 - Gray Eagle [11/01/2023]

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

Tool	Previous version	New version
isoseq3	3.4.0	3.8.1
lima	2.2.0	2.6.0
minimap2	2.21	2.24
samtools	1.12	1.14
multiqc	1.13	1.14
pbccs	6.2.0	6.4.0
ultra_bioinformatics	0.0.4	0.0.4.2
samtools	1.15.1	1.16.1

nf-core/isoseq v1.1.1 - White Hawk [26/09/2022]

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

• samplesheet_check
• dumpsoftwareversion
• MultiQC

Fix aligner option documentation.

nf-core/isoseq v1.1.0 - Black Crow [12/07/2022]

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

nf-core/isoseq v1.0.0 - Silver Swan [28/06/2022]

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