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Add schema validation for assemblysubmit and genomesubmit workflows

enhancementNew feature or requestNew feature or request

Status: Open.

#33 In nf-core/seqsubmit;

· ochkalova opened on Mar 6, 2026

Fix and improve tests for genome and assembly submission workflows

bugSomething isn't workingSomething isn't working

enhancementNew feature or requestNew feature or request

Status: Open.

#32 In nf-core/seqsubmit;

· ochkalova opened on Mar 6, 2026

Output the list of assigned accessions after pipeline execution

enhancementNew feature or requestNew feature or request

Status: Open.

#31 In nf-core/seqsubmit;

· ochkalova opened on Mar 5, 2026

Improve registerstudy module

enhancementNew feature or requestNew feature or request

Status: Open.

#30 In nf-core/seqsubmit;

· mberacochea opened on Mar 5, 2026

Accept assembly submissions for raw-reads not submitted to ENA

enhancementNew feature or requestNew feature or request

Status: Open.

#29 In nf-core/seqsubmit;

· KateSakharova opened on Feb 19, 2026

Add a subworkflow to upload raw reads to ENA

enhancementNew feature or requestNew feature or request

Status: Open.

#28 In nf-core/seqsubmit;

· mberacochea opened on Feb 12, 2026

[ENA] For metagenomic assemblies the pipeline should inform users that ERZ accessions are just temporary

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#25 In nf-core/seqsubmit;

· mberacochea opened on Nov 5, 2025

[ENA] For metagenomic assemblies we should keep track of the run-ref

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#24 In nf-core/seqsubmit;

· mberacochea opened on Nov 5, 2025

Add optional steps to genome_submit subworkflow to handle metadata (Taxonomy)

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#11 In nf-core/seqsubmit;

· KateSakharova opened on Oct 28, 2025

Add optional steps to genome_submit subworkflow to handle metadata (RNA)

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#10 In nf-core/seqsubmit;

· KateSakharova opened on Oct 28, 2025

Add optional steps to genome_submit subworkflow to handle metadata (coverm)

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#9 In nf-core/seqsubmit;

· KateSakharova opened on Oct 28, 2025

Add optional steps to genome_submit subworkflow to handle metadata (checkm2)

enhancementNew feature or requestNew feature or request

Status: Open.

Task

#7 In nf-core/seqsubmit;

· KateSakharova opened on Oct 24, 2025