nf-core/isoseq: 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 |