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": false,
      "type": "aggregated"
    },
    "per-read-bamstats": {
      "filepath": "./{{ alias }}.readstats.tsv",
      "title": "Per-read alignment stats",
      "description": "Bamstats per-read output TSV file.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "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"
    },
    "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"
    }
  }
}