output_definition.json

{
  "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 }}/config_stats.json",
      "title": "Results summaries",
      "description": "Results summaries including adapter configuration numbers.",
      "mime-type": "application/json",
      "optional": false,
      "type": "per-sample"
    },
    "gene-expression": {
      "filepath": "./{{ alias }}/gene_expression.counts.tsv",
      "title": "Gene expression counts",
      "description": "Gene x cell expression matrix.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "gene-expression-processed": {
      "filepath": "./{{ alias }}/gene_expression.processed.tsv",
      "title": "Processed gene expression counts",
      "description": "Filtered and normalized gene x cell expression matrix.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "transcript-expression": {
      "filepath": "./{{ alias }}/transcript_expression.counts.tsv",
      "title": "Transcript expression counts",
      "description": "Transcript x cell expression matrix.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "transcript-expression-processed": {
      "filepath": "./{{ alias }}/transcript_expression.processed.tsv",
      "title": "Processed transcript expression counts",
      "description": "Filtered and normalized transcript x cell expression matrix.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "mitochondrial-expression": {
      "filepath": "./{{ alias }}/gene_expression.mito.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-tags": {
      "filepath": "./{{ 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"
    },
    "barcode-counts": {
      "filepath": "./{{ alias }}/uncorrected_bc_counts.tsv",
      "title": "Barcode counts",
      "description": "The counts of each barcode present in the sequenced library (only barcodes that have a 100% match in the 10x whitelist are included).",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "whitelist": {
      "filepath": "./{{ 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 }}/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 }}/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 }}/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 }}/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"
    }
  }
}