output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "./wf-mpx-report.html",
      "title": "Workflow report",
      "description": "The report for the workflow",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "denovo-consensus-fasta" : {
      "filepath": "./denovo.consensus.fasta",
      "title": "De novo consensus assembly FASTA",
      "description": "De novo consensus assembly sequence from Flye and polished by Medaka.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "per-sample"
    },
    "draft-consensus-fasta" : {
      "filepath": "./{{ alias }}.ref.consensus.fasta",
      "title": "Reference-based consensus assembly FASTA",
      "description": "Reference-based consensus sequence from Bcftools.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "per-read-stats" : {
      "filepath": "./{{ alias }}.per-read-stats.tsv.gz",
      "title": "Read stats",
      "description": "A simple text file providing a summary of sequencing reads.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "read-alignment" : {
      "filepath": "./{{ alias }}.bam",
      "title": "Read alignment",
      "description": "Read alignments in BAM format.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "read-alignment-index": {
      "filepath": "./{{ alias }}.bam.bai",
      "title": "Alignment index file",
      "description": "Index file of BAM file.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "variants-file" : {
      "filepath": "./{{ alias }}.annotate.filtered.vcf",
      "title": "Variants file",
      "description": "Called variants in VCF format.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "depth-file" : {
      "filepath": "./{{ alias }}.annotate.filtered.vcf",
      "title": "Depth file",
      "description": "Per-base depth: overall, forward and reverse.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    }
  }
}