output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "./wf-artic-report.html",
      "title": "Workflow report",
      "description": "Report for all samples.",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "consensus": {
      "filepath": "./all_consensus.fasta",
      "title": "Consensus sequences",
      "description": "Final consensus sequences for all samples in the analysis.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "aggregated"
    },
    "pangolin-results": {
      "filepath": "./lineage_report.csv",
      "title": "Pangolin results",
      "description": "Pangolin results for each of the samples in the analysis.",
      "mime-type": "text/csv",
      "optional": false,
      "type": "aggregated"
    },
    "nextclade-results": {
      "filepath": "./nextclade.json",
      "title": "Nextclade results",
      "description": "Nextclade results for each of the samples in the analysis.",
      "mime-type": "application/json",
      "optional": false,
      "type": "aggregated"
    },
    "coverage": {
      "filepath": "./all_depth.txt",
      "title": "Coverage data",
      "description": "Coverage of the reference genome in 20 base windows in all the samples in the analysis.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "aggregated"
    },
    "variants": {
      "filepath": "./{{ alias }}.pass.named.vcf.gz",
      "title": "Variants",
      "description": "A VCF file containing high confidence variants in the sample when compared to the reference.",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "variants-index": {
      "filepath": "./{{ alias }}.pass.named.vcf.gz.tbi",
      "title": "Variants index",
      "description": "An index file for the variants.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "alignments": {
      "filepath": "./{{ alias }}.primertrimmed.rg.sorted.bam",
      "title": "Alignments",
      "description": "A BAM file containing the reads for the sample aligned to the reference.",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "alignments-index": {
      "filepath": "./{{ alias }}.primertrimmed.rg.sorted.bam.bai",
      "title": "Alignments index",
      "description": "An index file for the alignments.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    }
  }
}