output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "wf-bacterial-genomes-report.html",
      "title": "Workflow report",
      "description": "Report for all samples",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "workflow-results": {
      "filepath": "results.json",
      "title": "Workflow results",
      "description": "Structured workflow results for internal/onward use.",
      "mime-type": "text/json",
      "optional": false,
      "type": "aggregated"
    },
    "workflow-checkpoints" : {
      "filepath": "checkpoints.json",
      "title": "workflow checkpoints",
      "description": "Structured workflow checkpoints for internal/onward use.",
      "mime-type": "text/json",
      "optional": false,
      "type": "aggregated"
    },
    "sample-data": {
      "filepath": "{{ alias }}/seqs.fastq.gz",
      "title": "Concatenated sequence data",
      "description": "Per sample reads concatenated in to one fastq file.",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "read-stats-per-file": {
      "filepath": "{{ alias }}/fastcat_stats/per-file-stats.tsv",
      "title": "Per file read stats",
      "description": "A TSV with per file read stats, per sample.",
      "mime-type": "text/tsv",
      "optional": false,
      "type": "per-sample"
    },
    "read-stats-per-read": {
      "filepath": "{{ alias }}/fastcat_stats/per-read-stats.tsv.gz",
      "title": "Per read stats",
      "description": "A TSV with per read stats, per sample",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "alignment": {
      "filepath": "{{ alias }}.bam",
      "title": "alignment",
      "description": "Aligned reads for the sample in BAM format.",
      "mime-type": "application/x-gzip",
      "optional": true,
      "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": true,
      "type": "per-sample"
    },
    "assembly": {
      "filepath": "{{ alias }}.medaka.fasta.gz",
      "title": "Draft assembly FASTA file",
      "description": "Consensus file generated from either de-novo assembly or reference variant calling pipeline.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "variants": {
      "filepath": "{{ alias }}.medaka.vcf.gz",
      "title": "Variants VCF file",
      "description": "VCF file of variants detected against the provided reference (Reference mode only).",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "variants_stats": {
      "filepath": "{{ alias }}.variants.stats",
      "title": "Variants summary",
      "description": "TSV file of summary statistics for variants in sample (Reference mode only).",
      "mime-type": "text/tab-seperated-values",
      "optional": true,
      "type": "per-sample"
    },
    "annotation": {
      "filepath": "{{ alias }}.prokka.gff",
      "title": "Annotations files",
      "description": "Annotations of regions of interest in assembly in GBK and GFF format.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "mlst": {
      "filepath": "{{ alias }}.mlst.json",
      "title": "Sequence typing results",
      "description": "Sequence typing results in JSON format (isolates mode only).",
      "mime-type": "application/json",
      "optional": true,
      "type": "per-sample"
    },
    "amr": {
      "filepath": "{{ alias }}_resfinder_results",
      "title": "AMR calling results",
      "description": "Resfinder results for AMR calling (isolates mode only).",
      "mime-type": "inode/directory",
      "optional": true,
      "type": "per-sample"
    },
    "per-sample-report": {
      "filepath": "{{ alias }}-isolates-report.html",
      "title": "isolates per sample report",
      "description": "Per sample report isolates mode",
      "mime-type": "text/html",
      "optional": true,
      "type": "per-sample"
    }
  },
  "checkpoints": {
    "reads": {
      "type": "per-sample",
      "title": "reads",
      "description": "Checkpoint to monitor data ingress",
      "files": [
        "sample-data",
        "read-stats-per-file",
        "read-stats-per-read"
      ]
    },
    "alignment": {
      "type": "per-sample",
      "title": "alignment",
      "description": "Checkpoint to monitor alignment",
      "files": [
        "alignment",
        "alignment-index"
      ]
    },
    "assembly": {
      "type": "per-sample",
      "title": "assembly",
      "description": "Checkpoint to monitor alignment",
      "files": [
        "assembly"
      ]
    },
    "variant-calling": {
      "type": "per-sample",
      "title": "variant calling",
      "description": "Checkpoint to monitor variant calling",
      "files": [
        "variants"
      ]
    },
    "annotation": {
      "type": "per-sample",
      "title": "annotation",
      "description": "Checkpoint to monitor assembly annotation",
      "files": [
        "annotation"
      ]
    },
    "amr": {
      "type": "per-sample",
      "title": "Antimicrobial resistance ",
      "description": "Checkpoint to monitor amr",
      "files": [
        "mlst",
        "amr"
      ]
    },
    "reporting": {
      "type": "aggregated",
      "title": "reporting",
      "description": "Checkpoint to monitor reporting",
      "files": [
        "workflow-report",
        "workflow-results"
      ]
    },
    "per-sample-report": {
      "type": "per-sample",
      "title": "per-sample reporting",
      "description": "Checkpoint to monitor per-sample reporting",
      "files": [
        "per-sample-report"
      ]
    }
  }
}