Sequence File

Changelog for sequence_file.json

Minor changes since schema version 14

• Extend read_names enum list to include Barcode forward.
• Extend read_names enum list to include UMI.
• Extend read_names enum list to include Barcode reverse.
• Extend collections enum list to include IGVF_catalog_beta_v0.5.
• Add checkfiles_version.
• Extend sequencing_kit enum list to include AVITI 2x75 Sequencing Kit Cloudbreak High Output.
• Extend upload_status enum list to include validation exempted.
• Extend sequencing_kit enum list to include AVITI 2x150 Sequencing Kit Cloudbreak High Output.
• Extend status enum list to include preview.
• Add read_names.
• Extend base_modifications enum list to include inosine.
• Extend base_modifications enum list to include pseudouridine.
• Add external_host_url.
• Add externally_hosted.
• Add derived_manually.
• Extend collections enum list to include VarChAMP.
• Add calculated property assay_titles.
• Extend sequencing_kit enum list to include Singular G4 F2 Reagent Kit.
• Add base_modifications.
• Extend sequencing_kit enum list to include NovaSeq X Series 1.5B Reagent Kit.
• Extend sequencing_kit enum list to include NovaSeq X Series 25B Reagent Kit.
• Update calculation of summary.
• Add analysis_step_version.
• Add calculated property input_file_for.

Schema version 14

• Reduce upload_status enum list to exclude deposited.
• Remove anvil_source_url.
• Add anvil_url.
• Require controlled_access.

Schema version 13

• Adjust sequencing_kit enum list to replace NovaSeq 6000 S4 Reagent Kit V1.5 with NovaSeq 6000 S4 Reagent Kit v1.5.

Minor changes since schema version 12

• Extend sequencing_kit enum list to include ONT Ligation Sequencing Kit V14.
• Extend sequencing_kit enum list to include NovaSeq X Series 10B Reagent Kit.
• Extend sequencing_kit enum list to include MiSeq Reagent Kit v2.
• Extend sequencing_kit enum list to include NextSeq 1000/2000 P1 Reagent Kit.
• Extend sequencing_kit enum list to include NextSeq 1000/2000 P2 Reagent Kit.
• Extend sequencing_kit enum list to include NextSeq 1000/2000 P3 Reagent Kit.
• Extend collections enum list to include Vista.
• Extend collections enum list to include IGVF_catalog_beta_v0.2.
• Extend collections enum list to include IGVF_catalog_beta_v0.3.
• Extend collections enum list to include IGVF_catalog_beta_v0.4.

Schema version 12

• Extend upload_status enum list to include deposited.
• Add controlled_access.
• Add anvil_source_url.
• Add calculated property anvil_destination_url.

Minor changes since schema version 11

• Add sequencing_kit.

Schema version 11

• Require derived_from to contain at least one value.
• Require file_format_specifications to contain at least one value.

Schema version 10

• Require release_timestamp for any objects with released, archived, or revoked status.

Schema version 9

• Remove seqspec.
• Add calculated property seqspecs.

Minor changes since schema version 8

• Update aliases regex to add buenrostro-bernstein as a namespace.

Schema version 8

• Replace subreads with PacBio subreads in content_type.
• Expand content_type enum list to include Nanopore reads.

Minor changes since schema version 7

• Add release_timestamp.
• Add MPRAbase to collections.

Schema version 7

• Require publicly released files to have upload_status of validated or invalidated.

Schema version 6

• Disallow empty strings in description.

Minor changes since schema version 5

• Allow hyphens in dbxrefs.

Schema version 5

• Require a minimum of 1 item for dbxrefs.

Minor changes since schema version 4

• Add index.
• Expand collections enum list to include ClinGen, GREGoR, IGVF_catalog_beta_v0.1, and MaveDB.

Schema version 4

• Restrict minimum_read_length to a maximum value of 300000000.
• Restrict maximum_read_length to a maximum value of 300000000.
• Restrict mean_read_length to a maximum value of 300000000.
• Change mean_read_length type to number.

Minor changes since schema version 3

• Add seqspec.

Schema version 3

• Require sequencing_platform.
• Add flowcell_id and lane.