v0.6.0 – Bellsprout

[0.6.0] – Bellsprout – [2024-09-13]

The pipeline has now been validated for draft (unpublished) assemblies.

• The pipeline now queries the NCBI database instead of GoaT to establish the taxonomic classification of the species and the relevant Busco lineages. In case the taxon_id is not found, the pipeline falls back to GoaT, which is aware of upcoming taxon_ids in ENA.
• New --busco_lineages parameter to choose specific Busco lineages instead of automatically selecting based on the taxonomy.
• All parameters are now passed the regular Nextflow way. There is no support for the original Yaml configuration files of the Snakemake version.
• New option --skip_taxon_filtering to skip the taxon filtering in blast searches. Mostly relevant for draft assemblies.
• Introduced the --use_work_dir_as_temp parameter to avoid leaving files in /tmp.

Parameters

Old parameter	New parameter
--yaml
	--busco_lineages
	--skip_taxon_filtering
	--use_work_dir_as_temp

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
goat	0.2.5