v0.11.0 – Bulbasaur

Enhancements & fixes

• Added an option to control the version ("revision") of the blobDir.
  Use when rerunning the pipeline on an assembly.
• Restructured locations and names of output files, see output.md
• The sample samplesheet column can now contain / to organise the read_mapping/ outputs in sub-directories.
• Added parameter --window_size to partition sequences and calculate per-window statistics
• Updated blobtk/images to blobtk/plot (an nf-core module), and patched the module for version 0.8.1 which is not yet available via bioconda.
• Added the grid plot generation from blobtk/plot.
• Updated blast/blastn db path to be staged as a BLASTN_DB_DIR due to an edge case where : could cause a malformed path.
• Versions are now output via topic where possible (e.g. where tools are run prior to version collection).

Parameters

Old parameter	New parameter
	--revision
	--window_size

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. Only Docker or Singularity containers are supported, conda is not supported.

Dependency	Old version	New version
blast	2.15.0	2.17.0
blobtk	0.5.1	0.8.1
diamond	2.1.16	2.1.23
gunzip	1.1	1.13
minimap2	2.28	2.29
samtools	1.20 and 1.21	1.21 and 1.23.1

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.