v0.1.0 – Vaporeon

[0.1.0] – Vaporeon – [2023-05-18]

Enhancements & fixes

Initial release of sanger-tol/blobtoolkit 🎉

This release marks the point where the pipeline was moved from Snakemake at blobtoolkit/blobtoolkit over to Nextflow DSL2 at sanger-tol/blobtoolkit. There are two subworkflows in the Snakemake version that are still being implemented in Nextflow – diamond_blastx and blastn.

Parameters

Old parameter	New parameter
	--input
	--fasta
	--accession
	--taxon
	--taxa_file
	--yaml
	--blastp_outext
	--blastp_cols
	--taxdump
	--busco
	--uniprot

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

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
blobtoolkit		4.1.4
busco		5.4.3
fasta_windows		0.2.4
goat		0.2.0
gunzip		1.10
mosdepth		0.3.3
nextflow		22.10.6
python		3.10.6
samtools		1.15.1
tar		1.30
yaml		6.0

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.