wf-metagenomics/output_definition.json at master · epi2me-labs/wf-metagenomics · GitHub

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{
    "files": {
      "workflow-report": {
        "filepath": "wf-metagenomics-report.html",
        "title": "workflow report",
        "description": "Report for all samples.",
        "mime-type": "text/html",
        "optional": false,
        "type": "aggregated"
      },
      "abundance-table-rank": {
        "filepath": "abundance_table_{{ taxonomic_rank }}.tsv",
        "title": "Abundance table with counts per taxa",
        "description": "Per-taxa counts TSV, including all samples.",
        "mime-type": "text/tab-separated-values",
        "optional": false,
        "type": "aggregated"
      },
      "bracken-report": {
        "filepath": "bracken/{{ alias }}.kraken2_bracken.report",
        "title": "Bracken report file",
        "description": "TSV file with the abundance of each taxa. More info about [bracken report](https://github.com/jenniferlu717/Bracken#output-kraken-style-bracken-report).",
        "mime-type": "text/tab-separated-values",
        "optional": true,
        "type": "per-sample"
      },
      "kraken-report": {
        "filepath": "kraken2/{{ alias }}.kraken2.report.txt",
        "title": "Kraken2 taxonomic assignment per read (Kraken2 pipeline)",
        "description": "Lineage-aggregated counts. More info about [kraken2 report](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#sample-report-output-format).",
        "mime-type": "text/txt",
        "optional": true,
        "type": "per-sample"
      },
      "host-bam": {
        "filepath": "host_bam/{{ alias }}.bam",
        "title": "Host BAM file",
        "description": "BAM file generated from mapping filtered input reads to the host reference.",
        "mime-type": "application/gzip",
        "optional": true,
        "type": "per-sample"
      },
      "host-bai": {
        "filepath": "host_bam/{{ alias }}.bai",
        "title": "BAM index file of host reads",
        "description": "BAM index file generated from mapping filtered input reads to the host reference.",
        "mime-type": "application/octet-stream",
        "optional": true,
        "type": "per-sample"
      },
      "minimap2-bam": {
        "filepath": "bams/{{ alias }}.reference.bam",
        "title": "BAM file (minimap2)",
        "description": "BAM file generated from mapping filtered input reads to the reference.",
        "mime-type": "application/gzip",
        "optional": true,
        "type": "per-sample"
      },
      "minimap2-index": {
        "filepath": "bams/{{ alias }}.reference.bam.bai",
        "title": "BAM index file (minimap2)",
        "description": "Index file generated from mapping filtered input reads to the reference.",
        "mime-type": "application/octet-stream",
        "optional": true,
        "type": "per-sample"
      },
      "minimap2-flagstats": {
        "filepath": "bams/{{ alias }}.bamstats_results/bamstats.flagstat.tsv",
        "title": "BAM flagstat (minimap2)",
        "description": "Mapping results per reference",
        "mime-type": "text/tab-separated-values",
        "optional": true,
        "type": "per-sample"
      },
      "minimap2-bamreadstats": {
        "filepath": "bams/{{ alias }}.bamstats_results/bamstats.readstats.tsv.gz",
        "title": "Minimap2 alignment statistics (minimap2)",
        "description": "Per read stats after aligning",
        "mime-type": "application/gzip",
        "optional": true,
        "type": "per-sample"
      },
      "amr-report": {
        "filepath": "amr/{{ alias }}.json",
        "title": "JSON file with identified AMR genes (amr)",
        "description": "JSON file with abricate results. More info about [abricate output](https://github.com/tseemann/abricate#output).",
        "mime-type": "text/json",
        "optional": true,
        "type": "per-sample"
      },
      "reduced-reference": {
        "filepath": "igv_reference/reduced_reference.fasta.gz",
        "title": "Reduced reference FASTA file",
        "description": "Reference FASTA file containing only those sequences that have reads mapped against them.",
        "mime-type": "application/gzip",
        "optional": true,
        "type": "aggregated"
      },
      "reduced-reference-index": {
        "filepath": "igv_reference/reduced_reference.fasta.gz.fai",
        "title": "Index of the reduced reference FASTA file",
        "description": "Index of the reference FASTA file containing only those sequences that have reads mapped against them.",
        "mime-type": "text/tab-separated-values",
        "optional": true,
        "type": "aggregated"
      },
      "reduced-reference-gzi-index": {
        "filepath": "igv_reference/reduced_reference.fasta.gz.gzi",
        "title": "GZI index of the reduced reference FASTA file",
        "description": "Index of the reference FASTA file containing only those sequences that have reads mapped against them.",
        "mime-type": "application/octet-stream",
        "optional": true,
        "type": "aggregated"
      },
      "igv-config": {
        "filepath": "igv.json",
        "title": "JSON configuration file for IGV browser",
        "description": "JSON configuration file to be loaded in IGV for visualising alignments against the reduced reference.",
        "mime-type": "text/json",
        "optional": true,
        "type": "aggregated"
      },
      "kraken-read-assignments": {
        "filepath": "reads_assignments/{{ alias }}_lineages.kraken2.assignments.tsv",
        "title": "Taxonomic assignment per read from kraken2.",
        "description": "TSV file with the taxonomic assignment classified by kraken2 (no identity or coverage filters are applied).",
        "mime-type": "text/tab-separated-values",
        "optional": true,
        "type": "per-sample"
      },
      "minimap-read-assignments": {
        "filepath": "reads_assignments/{{ alias }}_lineages.minimap2.assignments.tsv",
        "title": "Taxonomic assignment per read from minimap2.",
        "description": "TSV file with the taxonomic assignment per read after identity and coverage filters.",
        "mime-type": "text/tab-separated-values",
        "optional": true,
        "type": "per-sample"
      },
      "extracted-fastq": {
        "filepath": "extracted/{{ alias }}.minimap2.extracted.fastq",
        "title": "FASTQ of the selected taxids.",
        "description": "FASTQ containing/excluding the reads of the selected taxids.",
        "mime-type": "text",
        "optional": true,
        "type": "per-sample"
      },
      "unclassified-fastq": {
        "filepath": "unclassified/{{ alias }}.unclassified.fq.gz",
        "title": "FASTQ of the unclassified reads.",
        "description": "FASTQ containing the reads that have not been classified against the database.",
        "mime-type": "application/gzip",
        "optional": true,
        "type": "per-sample"
      },
      "alignment-table": {
        "filepath": "alignment_tables/{{ alias }}.alignment-stats.tsv",
        "title": "TSV with some alignment statistics",
        "description": "Coverage and taxonomy of each reference.",
        "mime-type": "text/tab-separated-values",
        "optional": true,
        "type": "per-sample"
      }
    }
  }