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CHANGELOG.md

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sanger-tol/ear: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning. Naming based on: Audiologists.

v0.7.0 - Raymond Carhart [12/02/2025]

  • Removing the mapping subworkflow as it is no longer needed.
    • This was a requirement before BLOBTOOLKIT implemented it's own mapping subworkflow.
    • This significantly speeds up the pipeline in two ways.
      • We no longer have to wait for mapping to complete prior to BTK.
      • BTK doesn't have to struggle with the much larger mapped bam that was being created.
  • NF-TEST implementation.
    • We have implemented an output file sanity check rather than rely soley on pipeline completion.

Software dependencies

No Software updates

Parameters

Old parameter New parameter
--mapped

KNOWN BUG

  • BLOBTOOLKIT relies on BUSCO 5.5, which does NOT run with single line fasta!
    • This needs to be folded, use seqkit seq -l 70

v0.6.2 - Robert Beiny H2 [09/01/2025]

  • Modules have been updated to remove conda defaults.

Software dependencies

Dependency Old version New version
sanger-tol/blobtoolkit* 0.6.0 (Bellsprout)
sanger-tol/curationpretext* 1.0.0 (UNSC Cradle) 1.1.0 (UNSC Delphi)
GFASTATS 1.3.6--hdcf5f25_3
MERQUERY_FK 1.2
MINIMAP2_ALIGN 2.28
SAMTOOLS_MERGE 1.20--h50ea8bc_0 1.21--h50ea8bc_0
SAMTOOLS_SORT 1.21--h50ea8bc_0 1.21--h50ea8bc_0

v0.6.1 - Robert Beiny H1 [08/10/2024]

  • Blobtookit version was specified in the wrong location, so defaulted to a development branch "draft_assemblies", this has now been updated to v0.6.0.
  • Zenodo DOI has now been added to the repo.

v0.6.0 - Robert Beiny [20/09/2024]

Initial release of sanger-tol/ear, created with the nf-core template. The current pipeline means the MVP for ear.

Added

GFASTATS to generate statistics on the input primary genome. MERQURY_FK to generate kmer graphs and analyses of the primary, haplotype and merged assembly. MAIN_MAPPING which is a small mapping subworkflow, that can work with single and paired reads. BLOBTOOLKIT to generate busco files and blobtoolkit dataset/plots. CURATIONPRETEXT to generate pretext plots and pngs.

Parameters

Old parameter New parameter
--mapped
--steps

Software dependencies

Dependency Old version New version
sanger-tol/blobtoolkit* 0.6.0 (Bellsprout)
sanger-tol/curationpretext* 1.0.0 (UNSC Cradle)
GFASTATS 1.3.6--hdcf5f25_3
MERQUERY_FK 1.2
MINIMAP2_ALIGN 2.28
SAMTOOLS_MERGE 1.20--h50ea8bc_0
SAMTOOLS_SORT 1.20--h50ea8bc_0

* for pipelines, please check their own CHANGELOG file for a full list of software dependencies.

Dependencies

The pipeline depends on a number of databases which are noted in README and USAGE.