output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "./wf-tb-amr-report.html",
      "title": "Workflow report",
      "description": "The report for all samples in the workflow run",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "workflow-csv-summary": {
      "filepath": "./wf-tb-amr-report.csv",
      "title": "Workflow CSV results summary",
      "description": "The CSV summary of the results of the workflow",
      "mime-type": "text/csv",
      "optional": false,
      "type": "aggregated"
    },
    "alignment": {
      "filepath": "./{{ alias }}.bam",
      "title": "Alignment",
      "description": "Aligned reads for the sample in BAM format",
      "mime-type": "application/x-gzip",
      "optional": false,
      "type": "per-sample"
    },
    "alignment-index": {
      "filepath": "./{{ alias }}.bam.bai",
      "title": "Alignment index",
      "description": "An index file for the alignment in BAI format",
      "mime-type": "application/x-gzip",
      "optional": false,
      "type": "per-sample"
    },
    "variants": {
      "filepath": "./{{ alias }}.final.vcf",
      "title": "Variants",
      "description": "Called, annotated variants for the sample.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "per-sample-report": {
      "filepath": "./{{ alias }}_report.html",
      "title": "Per sample report",
      "description": "The report for a single sample",
      "mime-type": "text/html",
      "optional": false,
      "type": "per-sample"
    }
  }
}