Release Notes:

Webin-CLI – BioSamples Validation Update

Previously, Webin-CLI validated BioSamples submissions by requiring a taxID in the sample metadata. However, BioSamples does not enforce taxID in its JSON schemas. Instead, it requires each sample to provide an Organism attribute.

With this update, Webin-CLI has been adapted to validate BioSamples submissions by checking for the Organism attribute rather than relying on taxID. The taxID requirement now applies only when samples are destined for ENA, in which case the taxID is validated through Webin REST to ensure correctness and submittability. This change aligns Webin-CLI validation with BioSamples schema rules while maintaining strict taxID checks for ENA submissions.

Release notes:

• genome context : File group permission changes. FASTA and FLATFILE files are not allowed to by sent together in the same submission. See webin-cli help for more information.

Release notes:

PolySample context

Support has been introduced for submissions involving environmental sequence sets associated with multiple samples and taxonomic annotations. This context enables submission of a FASTA file containing sequences, a SAMPLE_TSV file mapping sequences to samples, and optionally a TAX_TSV file mapping sequences to taxa.

The following file group combinations are supported:

• 1 FASTA + 1 SAMPLE_TSV + 1 TAX_TSV
• 1 FASTA + 1 SAMPLE_TSV
• 1 TAX_TSV

New metadata fields have been added to support enriched environmental sequence submissions. These include:

• ANALYSIS_TYPE: Type of SEQUENCE_SET, currently supported value is ENVIRONMENTAL_SEQUENCE_SET. (Required when applicable.)
• ANALYSIS_PROTOCOL: Free-text protocol description.
• ANALYSIS_DATE: Date of analysis.
• TARGET LOCUS: Name of the targeted genetic locus.
• ANALYSIS CODE: Code identifying the analysis.
• ANALYSIS VERSION: Version number of the analysis.
• ORGANELLE: Organelle from which the sequences originated.
• FORWARD PRIMER NAME: Name of the forward primer.
• FORWARD PRIMER SEQUENCE: Sequence of the forward primer.
• REVERSE PRIMER NAME: Name of the reverse primer.
• REVERSE PRIMER SEQUENCE: Sequence of the reverse primer.
• ANALYSIS CENTER: Name of the analysis center.

These fields enhance the ability to capture detailed metadata required for multi-sample, sequence-based environmental analyses.

Release notes:

• Sequence context: Support has been introduced for the Environmental Sequence Set (ENVIRONMENTAL_SEQUENCE_SET) analysis type. This newly added analysis type enables users to submit a FASTA file containing sequences, along with a TSV file that maps each sequence to one or more samples while also specifying the frequency of each sequence within the associated samples.

• Sequence context: A new optional manifest field, ANALYSIS_TYPE, has been introduced. If a submission pertains to an ENVIRONMENTAL_SEQUENCE_SET analysis, the ANALYSIS_TYPE field is mandatory. The expected value for ANALYSIS_TYPE in this context is SEQUENCE_SET.

Release notes:

• Read context: added support for Illumina NovaSeq X Plus and DNBSEQ-T10×4RS instrument model.
• Genome context: block submissions with chromosome names specified as "contig" or "scaffold"
• Genome context: Enhancements to prevent overlapping gaps.

Release notes:

• genome context : AGP file support has been removed.
• All contexts : General security updates.

Release notes:

• All contexts : Only supports Java 17 and above.
• read context : uses latest tools for file processing.
• read context : bz2 compressed file format is now supported.
• read context : fixes how NOT_AUTCG characters are counted. previously it was per read and not per sample, which was incorrect.
• read context : other improvements and fixes.

Release notes:

• All contexts: Resolved an issue with the taxonomy API, which was causing the following error:
  Error while calling the url: http://wwwint.ebi.ac.uk/ena/taxonomy/rest/

Release notes:

• genome, transcriptome and sequence contexts: Support new qualifier /geo_loc_name as a replacement for the /country qualifier. Any /country qualifiers will be automatically converted to /geo_loc_name qualifier.

Release notes:

• genome and sequence contexts: Fixed the following error from being erroneously reported when the feature was 5' partial: Protein coding feature can be a single stop codon only if it has 3 bases and is 5' partial.
• genome and sequence contexts: Fixed a bug where partiality was erroneously rejected when using the order operator
• genome and sequence contexts: Fixed the following error from being erroneously reported: Anticodon amino acid abbreviation "..." is not matching with the sequence "..." using translation table "...".