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output_definition.json
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{
"files": {
"workflow-report": {
"filepath": "wf-single-cell-report.html",
"title": "workflow report",
"description": "Report for all samples",
"mime-type": "text/html",
"optional": false,
"type": "aggregated"
},
"results-summary": {
"filepath": "{{ alias }}/{{ alias }}.config_stats.json",
"title": "Results summaries",
"description": "Results summaries including adapter configuration numbers.",
"mime-type": "application/json",
"optional": false,
"type": "per-sample"
},
"gene-expression-matrix": {
"filepath": "{{ alias }}/{{ alias }}.gene_raw_feature_bc_matrix/matrix.mtx.gz",
"title": "Gene expression counts",
"description": "Gene x cell expression sparse matrix values (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"gene-expression-barcodes": {
"filepath": "{{ alias }}/{{ alias }}.gene_raw_feature_bc_matrix/barcodes.tsv.gz",
"title": "Gene expression barcodes",
"description": "Barcode column names (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"gene-expression-features": {
"filepath": "{{ alias }}/{{ alias }}.gene_raw_feature_bc_matrix/features.tsv.gz",
"title": "Gene expression features",
"description": "Feature row names (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcript-expression-matrix": {
"filepath": "{{ alias }}/{{ alias }}.transcript_raw_feature_bc_matrix/matrix.mtx.gz",
"title": "Transcript expression counts",
"description": "Transcript x cell expression sparse matrix values (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcript-expression-barcodes": {
"filepath": "{{ alias }}/{{ alias }}.transcript_raw_feature_bc_matrix/barcodes.tsv.gz",
"title": "Transcript expression MEX barcodes",
"description": "Barcode column names (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcript-expression-features": {
"filepath": "{{ alias }}/{{ alias }}.transcript_raw_feature_bc_matrix/features.tsv.gz",
"title": "Transcript expression MEX features",
"description": "Feature row names (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"gene-processed-expression-matrix": {
"filepath": "{{ alias }}/{{ alias }}.gene_processed_feature_bc_matrix/matrix.mtx.gz",
"title": "Processed gene expression counts",
"description": "Filtered and normalized gene x cell expression sparse matrix values (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"gene-processed-expression-barcodes": {
"filepath": "{{ alias }}/{{ alias }}.gene_processed_feature_bc_matrix/barcodes.tsv.gz",
"title": "Processed gene expression barcodes",
"description": "Barcode column names (MEX format) for processed matrix.",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"gene-processed-expression-features": {
"filepath": "{{ alias }}/{{ alias }}.gene_processed_feature_bc_matrix/features.tsv.gz",
"title": "Processed gene expression features",
"description": "Feature row names (MEX format) for processed matrix.",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcript-processed-expression-matrix": {
"filepath": "{{ alias }}/{{ alias }}.transcript_processed_feature_bc_matrix/matrix.mtx.gz",
"title": "Processed transcript expression counts",
"description": "Filtered and normalized transcript x cell expression sparse matrix values (MEX format).",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcript-processed-expression-barcodes": {
"filepath": "{{ alias }}/{{ alias }}.transcript_processed_feature_bc_matrix/barcodes.tsv.gz",
"title": "Processed transcript expression MEX barcodes",
"description": "Barcode column names (MEX format) for processed matrix.",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcript-processed-expression-features": {
"filepath": "{{ alias }}/{{ alias }}.transcript_processed_feature_bc_matrix/features.tsv.gz",
"title": "Processed transcript expression MEX features",
"description": "Feature row names (MEX format) for processed matrix.",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"mitochondrial-expression": {
"filepath": "{{ alias }}/{{ alias }}.gene_expression_mito_per_cell.tsv",
"title": "Mitochondrial expression levels",
"description": "Per cell mitochondrial gene expression as percentage total of total gene expression.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"read-summary": {
"filepath": "{{ alias }}/{{ alias }}.read_summary.tsv",
"title": "Read summary",
"description": "Per read assigned barcodes UMIs genes and transcripts.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"whitelist": {
"filepath": "{{ alias }}/{{ alias }}.whitelist.tsv",
"title": "Whitelist",
"description": "The barcodes found in the library that remain after filtering.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "per-sample"
},
"alignment": {
"filepath": "{{ alias }}/{{ alias }}.tagged.bam",
"title": "Alignment output per sample",
"description": "Genomic alignment output file.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"alignment-index": {
"filepath": "{{ alias }}/{{ alias }}.tagged.bam.bai",
"title": "Alignment index per sample",
"description": "Genomic alignment index file.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"transcriptome_fasta": {
"filepath": "{{ alias }}/{{ alias }}.transcriptome.fa.gz",
"title": "Transcriptome sequence",
"description": "Transcriptome generated by Stringtie during transcript discovery stage",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"transcriptome_annotation": {
"filepath": "{{ alias }}/{{ alias }}.transcriptome.gff.gz",
"title": "Transcriptome annotation",
"description": "Transcriptome annotation generated by Stringtie during transcript discovery stage",
"mime-type": "application/gzip",
"optional": false,
"type": "per-sample"
},
"gene_expression_umap": {
"filepath": "{{ alias }}/{{ alias }}.gene_expression_umap_*.tsv",
"title": "Gene expression umap",
"description": "UMAP matrix from gene expression. Varying number of files will be present based on number of umap repeats.",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
},
"transcript_expression_umap": {
"filepath": "{{ alias }}/{{ alias }}.transcript_expression_umap_*.tsv",
"title": "Transcript expression umap",
"description": "UMAP matrix from transcript expression. Varying number of files will be present based on number of umap repeats.",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
},
"barcode_assignment_summary.tsv": {
"filepath": "{{ alias }}/{{ alias }}.bc_assignment_summary.tsv",
"title": "Barcode assignment summary",
"description": "TSV file with barcode assignment summary statistics.",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
}
}
}