output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "wf-alignment-report.html",
      "title": "workflow report",
      "description": "Report for all samples",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "references": {
      "filepath": "combined_refs.fasta",
      "title": "Combined references",
      "description": "FASTA file containing all input references.",
      "mime-type": "text/txt",
      "optional": false,
      "type": "aggregated"
    },
    "references-index": {
      "filepath": "combined_refs.fasta.fai",
      "title": "Combined references index",
      "description": "Index file for combined references FASTA.",
      "mime-type": "text/txt",
      "optional": false,
      "type": "aggregated"
    },
    "references-mmi-index": {
      "filepath": "combined_refs.mmi",
      "title": "Combined references MMI index",
      "description": "Minimap2 index file for combined references FASTA.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "aggregated"
    },
    "per-read-bamstats": {
      "filepath": "{{ alias }}.readstats.tsv.gz",
      "title": "Per-read alignment stats",
      "description": "Bamstats per-read output TSV file (compressed with gzip).",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "bamstats-flagstat": {
      "filepath": "{{ alias }}.flagstat.tsv",
      "title": "Per-reference alignment stats",
      "description": "Bamstats flagstat output TSV file.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "alignment-accuracy-histogram": {
      "filepath": "{{ alias }}-histograms/accuracy.hist",
      "title": "Alignment accuracy histogram",
      "description": "Bamstats alignment accuracy histogram TSV file.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "alignment-coverage-histogram": {
      "filepath": "{{ alias }}-histograms/coverage.hist",
      "title": "Alignment coverage histogram",
      "description": "Bamstats alignment coverage histogram TSV file.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "mapped-read-length-histogram": {
      "filepath": "{{ alias }}-histograms/length.hist",
      "title": "Read length histogram (mapped)",
      "description": "Bamstats read length histogram TSV file (for mapped reads).",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "unmapped-read-length-histogram": {
      "filepath": "{{ alias }}-histograms/length.unmap.hist",
      "title": "Read length histogram (unmapped)",
      "description": "Bamstats read length histogram TSV file (for unmapped reads).",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "mapped-read-quality-histogram": {
      "filepath": "{{ alias }}-histograms/quality.hist",
      "title": "Read quality histogram (mapped)",
      "description": "Bamstats read quality histogram TSV file (for mapped reads).",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "unmapped-read-quality-histogram": {
      "filepath": "{{ alias }}-histograms/quality.unmap.hist",
      "title": "Read quality histogram (unmapped)",
      "description": "Bamstats read quality histogram TSV file (for unmapped reads).",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "alignments": {
      "filepath": "{{ alias }}.sorted.aligned.bam",
      "title": "Alignments BAM file",
      "description": "BAM file with alignments of filtered input reads against the combined references.",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "alignments-index": {
      "filepath": "{{ alias }}.sorted.aligned.bam.bai",
      "title": "Alignments index file",
      "description": "Index for alignments BAM file.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "igv-config": {
      "filepath": "igv.json",
      "title": "IGV config JSON file",
      "description": "JSON file with IGV config options to be used by the EPI2ME Desktop Application.",
      "mime-type": "application/json",
      "optional": true,
      "type": "aggregated"
    }
  }
}