output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "./wf-clone-validation-report.html",
      "title": "worfklow report",
      "description": "A report bringing together the main results of the workflow, across samples.",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "sample-status-csv-summary": {
      "filepath": "./sample_status.txt",
      "title": "sample status",
      "description": "A CSV file with per-sample assembly success or failure reasons",
      "mime-type": "text/csv",
      "optional": false,
      "type": "aggregated"
    },
    "plannotate-annotations": {
      "filepath": "./plannotate.json",
      "title": "plasmid annotations",
      "description": "Plasmid annotations in a JSON structure.",
      "mime-type": "text/json",
      "optional": false,
      "type": "aggregated"
    },
    "annotations_bed" : {
      "filepath": "./{{ alias }}.annotations.bed",
      "title": "annotations bed",
      "description": "Plasmid annotations in a BED file format for onward use",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "annotations_gbk" : {
      "filepath": "./{{ alias }}.annotations.gbk",
      "title": "annotations gbk",
      "description": "Plasmid annotations in a GBK file format for onward use",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "assembly_fastq" : {
      "filepath": "./{{ alias }}.final.fastq",
      "title": "Assembly FASTQ",
      "description": "Sequence and quality score of the final assembly.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "assembly_stats": {
      "filepath": "./{{ alias }}.assembly_stats.tsv",
      "title": "Assembly statistics",
      "description": "Assembly statistics from fastcat.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "per-sample"
    },
    "insert_fasta" : {
      "filepath": "./{{ alias }}.insert.fasta",
      "title": "Insert FASTA",
      "description": "Insert sequence found in the final assembly, only relevant if the primers parameter was used.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "per-sample"
    },
    "variant_stats" : {
      "filepath": "./{{ alias }}.full_construct.stats",
      "title": "Variant stats report",
      "description": "A BCF stats report with any variants found, only relevant if a full reference was provided.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "per-sample"
    },
    "bcf" : {
      "filepath": "./{{ alias }}.full_construct.calls.bcf",
      "title": "Variants BCF file",
      "description": "A BCF file with any variants found per sample, only relevant if a full reference was provided.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "bam" : {
      "filepath": "./{{ alias }}.bam",
      "title": "Reference alignment",
      "description": "Reference aligned with the assembly in BAM format, only relevant if a full reference was provided.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "bai" : {
      "filepath": "./{{ alias }}.bam.bai",
      "title": "Reference alignment index",
      "description": "The index for the reference aligned with the assembly, only relevant if a full reference was provided.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "bam_stats" : {
      "filepath": "./{{ alias }}.bam.stats",
      "title": "BAM Stats",
      "description": "Stats report for the reference aligned with the assembly, only relevant if a full reference was provided.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "per-sample"
    }
  }
}