v1.2.0 - Pyrenean Mountain Dog

[1.2.0] - Pyrenean Mountain Dog - [2024-05-01]

Enhancements & fixes

• Updated the MerquryFK resources to cope with mistletoe (the pipeline as a
  whole is not yet fully compatible with mistletoe, though).
• Updated the Busco resources to better deal with large genomes.
• Round the chromosome lengths to 2 decimal points.
• The pipeline is now publishing the Busco output directories.
• The pipeline now generates a contact map for each Hi-C sample (instead of
  randomly picking one) and reports them all in the CSV.
• The Hi-C contact map is now ordered according to the karyotype (as defined in
  the assembly record) by default, and added the --cool_order option to
  override it.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Old version	New version
busco	5.4.3	5.5.0

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

Parameters

Old parameter	New parameter
	--cool_order