Analysis Step

Changelog for analysis_step.json

Minor changes since schema version 5

• Extend analysis_step_types enum list to include read trimming.
• Extend analysis_step_types enum list to include fastq concatenation.
• Extend analysis_step_types enum list to include fragment generation.
• Extend analysis_step_types enum list to include UMI deduplication.
• Extend analysis_step_types enum list to include matrix generation.
• Extend output_content_types enum list to include DNA footprint scores.
• Extend input_content_types enum list to include DNA footprint scores.
• Extend output_content_types enum list to include sequence attributes.
• Extend input_content_types enum list to include sequence attributes.
• Extend output_content_types enum list to include TF binding scores.
• Extend input_content_types enum list to include TF binding scores.
• Extend output_content_types enum list to include cell hashing barcodes.
• Extend input_content_types enum list to include cell hashing barcodes.
• Extend output_content_types enum list to include unfiltered local differential expression.
• Extend input_content_types enum list to include unfiltered local differential expression.
• Extend output_content_types enum list to include unfiltered global differential expression.
• Extend input_content_types enum list to include unfiltered global differential expression.
• Extend analysis_step_types enum list to include differential expression analysis.
• Extend analysis_step_types enum list to include demultiplexing.
• Extend analysis_step_types enum list to include cell to feature barcode mapping.
• Extend analysis_step_types enum list to include UMI quantification.
• Extend analysis_step_types enum list to include barcode counting.
• Extend status enum list to include preview.
• Extend output_content_types enum list to include barcode onlist.
• Extend input_content_types enum list to include barcode onlist.
• Extend output_content_types enum list to include differential chromatin contact quantifications.
• Extend input_content_types enum list to include differential chromatin contact quantifications.
• Extend output_content_types enum list to include variant functional predictions.
• Extend input_content_types enum list to include variant functional predictions.
• Extend output_content_types enum list to include bin paired count.
• Extend input_content_types enum list to include bin paired count.
• Extend analysis_step_types enum list to include base calling.
• Add calculated property analysis_step_versions.
• Extend output_content_types enum list to include reporter elements.
• Extend input_content_types enum list to include reporter elements.
• Extend output_content_types enum list to include reporter experiment.
• Extend input_content_types enum list to include reporter experiment.
• Extend output_content_types enum list to include reporter variants.
• Extend input_content_types enum list to include reporter variants.
• Extend output_content_types enum list to include reporter genomic element effects.
• Extend input_content_types enum list to include reporter genomic element effects .
• Extend output_content_types enum list to include reporter genomic variant effects.
• Extend input_content_types enum list to include reporter genomic variant effects.
• Extend input_content_types enum list to include differential element quantifications.
• Extend output_content_types enum list to include differential element quantifications.
• Extend input_content_types enum list to include model parameters.
• Extend output_content_types enum list to include model parameters.
• Extend analysis_step_types enum list to include counts normalization.
• Extend input_content_types enum list to include barcode to TF overexpression mapping.
• Extend output_content_types enum list to include barcode to TF overexpression mapping.
• Extend input_content_types enum list to include coding variant effects.
• Extend output_content_types enum list to include coding variant effects.
• Extend input_content_types enum list to include peak quantifications.
• Extend output_content_types enum list to include peak quantifications.
• Extend input_content_types enum list to include variant localization impacts.
• Extend output_content_types enum list to include variant localization impacts.
• Extend input_content_types enum list to include external source data.
• Extend input_content_types enum list to include fragments.
• Extend input_content_types enum list to include gene quantifications.
• Extend output_content_types enum list to include external source data.
• Extend output_content_types enum list to include fragments.
• Extend output_content_types enum list to include gene quantifications.
• Extend input_content_types enum list to include genes.
• Extend input_content_types enum list to include loci.
• Extend output_content_types enum list to include genes.
• Extend output_content_types enum list to include loci.
• Extend input_content_types enum list to include transcript quantifications.
• Extend input_content_types enum list to include barcode to hashtag mapping.
• Extend input_content_types enum list to include barcode to variant mapping.
• Extend output_content_types enum list to include transcript quantifications.
• Extend output_content_types enum list to include barcode to hashtag mapping.
• Extend output_content_types enum list to include barcode to variant mapping.
• Extend analysis_step_types enum list to include barcode mapping generation.
• Extend analysis_step_types enum list to include filtering.
• Extend analysis_step_types enum list to include interaction calling.
• Extend analysis_step_types enum list to include merging.
• Extend analysis_step_types enum list to include peak calling.
• Extend analysis_step_types enum list to include quantification.
• Extend analysis_step_types enum list to include signal normalization.
• Extend analysis_step_types enum list to include spatial feature detection.
• Extend analysis_step_types enum list to include variant annotation.
• Extend input_content_types enum list to include peaks.
• Extend input_content_types enum list to include detected tissue.
• Extend input_content_types enum list to include low resolution tissue.
• Extend input_content_types enum list to include high resolution tissue.
• Extend input_content_types enum list to include fiducial alignment.
• Extend input_content_types enum list to include edge weights.
• Extend input_content_types enum list to include graph structure.
• Extend input_content_types enum list to include position weight matrix.
• Extend input_content_types enum list to include barcode to element mapping.
• Extend input_content_types enum list to include barcode to sample mapping.
• Extend input_content_types enum list to include differential gene expression quantifications.
• Extend input_content_types enum list to include differential transcript expression quantifications.
• Extend input_content_types enum list to include editing templates.
• Extend input_content_types enum list to include element quantifications.
• Extend input_content_types enum list to include elements reference.
• Extend input_content_types enum list to include fold change over control.
• Extend input_content_types enum list to include guide quantifications.
• Extend input_content_types enum list to include guide RNA sequences.
• Extend input_content_types enum list to include MPRA sequence designs.
• Extend input_content_types enum list to include prime editing guide RNA sequences.
• Extend input_content_types enum list to include protein to protein interaction score.
• Extend input_content_types enum list to include tissue positions.
• Extend input_content_types enum list to include sample sort parameters.
• Extend input_content_types enum list to include sequence barcodes.
• Extend input_content_types enum list to include SNP effect matrix.
• Extend input_content_types enum list to include variants.
• Extend input_content_types enum list to include variant effects.
• Extend input_content_types enum list to include variant to element mapping.
• Extend output_content_types enum list to include peaks.
• Extend output_content_types enum list to include detected tissue.
• Extend output_content_types enum list to include low resolution tissue.
• Extend output_content_types enum list to include high resolution tissue.
• Extend output_content_types enum list to include fiducial alignment.
• Extend output_content_types enum list to include edge weights.
• Extend output_content_types enum list to include graph structure.
• Extend output_content_types enum list to include position weight matrix.
• Extend output_content_types enum list to include barcode to element mapping.
• Extend output_content_types enum list to include barcode to sample mapping.
• Extend output_content_types enum list to include differential gene expression quantifications.
• Extend output_content_types enum list to include differential transcript expression quantifications.
• Extend output_content_types enum list to include editing templates.
• Extend output_content_types enum list to include element quantifications.
• Extend output_content_types enum list to include elements reference.
• Extend output_content_types enum list to include fold change over control.
• Extend output_content_types enum list to include guide quantifications.
• Extend output_content_types enum list to include guide RNA sequences.
• Extend output_content_types enum list to include MPRA sequence designs.
• Extend output_content_types enum list to include prime editing guide RNA sequences.
• Extend output_content_types enum list to include protein to protein interaction score.
• Extend output_content_types enum list to include tissue positions.
• Extend output_content_types enum list to include sample sort parameters.
• Extend output_content_types enum list to include sequence barcodes.
• Extend output_content_types enum list to include SNP effect matrix.
• Extend output_content_types enum list to include variants.
• Extend output_content_types enum list to include variant effects.
• Extend output_content_types enum list to include variant to element mapping.

Schema version 5

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

Minor changes since schema version 4

• Update aliases regex to add buenrostro-bernstein as a namespace.
• Add release_timestamp.
• Add archived to status.

Schema version 4

• Disallow empty strings in description.

Schema version 3

• Require lab and award.

Schema version 2

• Require a minimum of 1 item for analysis_step_types, parents, input_content_types, and output_content_types.

Minor changes since schema version 1

• Add seqspec, contact matrix, sparse gene count matrix, sparse peak count matrix, sparse transcript count matrix, and transcriptome annotations to input_content_types and output_content_types.