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

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@sguizard sguizard released this 05 Sep 16:17
2.0.0
c7536ab
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Learn about vigilant mode.
  • 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
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