output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "./wf-flu-report.html",
      "title": "Workflow report",
      "description": "Easy-to-use HTML report for all samples in the run.",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "typing-results": {
      "filepath": "./wf-flu-results.csv",
      "title": "Typing results",
      "description": "Typing results in CSV format for onward processing.",
      "mime-type": "text/txt",
      "optional": false,
      "type": "aggregated"
    },
    "alignment": {
      "filepath": "./{{ alias }}/alignments/align.bam",
      "title": "Read alignments",
      "description": "Read allignments per sample in BAM format.",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "draft_consensus_fasta" : {
      "filepath": "./{{ alias }}/consensus/draft.consensus.fasta",
      "title": "Draft consensus FASTA",
      "description": "Draft consensus sequence.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "depth": {
      "filepath": "./{{ alias }}/coverage/depth.txt",
      "title": "Read depth",
      "description": "Read depth per base.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "typing": {
      "filepath": "./{{ alias }}/typing/insaflu.typing.txt",
      "title": "Insaflu typing results",
      "description": "Insaflu abricate typing results.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "variants-file" : {
      "filepath": "./{{ alias }}/variants/variants.annotated.filtered.vcf",
      "title": "Variants file",
      "description": "Called variants in VCF format.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    }
  }
}