v2.0.0 - English Cocker Spaniel

[2.0.0] - English Cocker Spaniel [2024-10-10]

Enhancements & fixes

• New genome_metadata subworkflow to fetch metadata linked to the genome assembly from various sources (COPO, GoaT, GBIF, ENA, NCBI). The options --assembly, --biosample_wgs, --biosample_hic and --biosample_rna specify what metadata to fetch and process.
• Now outputs a partially completed genome note document based on a template file which contains placeholder parameters. These placeholders are replaced with data generated by the pipeline. The template file to use can be specified using the --note_template option.
• Added the --write_to_portal option to write a set of key-value data parameters to a Genome Notes database.
• Added the --upload_higlass_data option to automatically upload the Hi-C Map to a kubernetes hosted Hi-Glass server.
• Bugfix: don't rely on fasta file name to correctly set assembly accession needed for use with ncbi datasets.
• Bugfix: ensure meta.id is used consistently.

Parameters

Old parameter	New parameter
	--assembly
	--biosample_wgs
	--biosample_hic
	--biosample_rna
	--write_to_portal
	--genome_notes_api
	--note_template
	--upload_higlass_data
	--higlass_url
	--higlass_deployment_name
	--higlass_namespace
	--higlass_kubeconfig
	--higlass_upload_directory
	--higlass_data_project_dir