output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "wf-basecalling-report.html",
      "title": "workflow report",
      "description": "Report summarising the work done by the basecalling workflow",
      "mime-type": "text/html",
      "optional": false,
      "type": "per-sample"
    },
    "simplex-alignment-pass": {
      "filepath": "{{ alias }}.pass.simplex.{{ format }}",
      "title": "Simplex alignment file of passed reads",
      "description": "BAM or CRAM file of simplex reads for the sample that pass QC filtering.",
      "mime-type": "application/x-gzip",
      "optional": false,
      "type": "per-sample"
    },    
    "duplex-alignment-pass": {
      "filepath": "{{ alias }}.pass.duplex.{{ format }}",
      "title": "Duplex alignment file of passed reads",
      "description": "BAM or CRAM file of duplex reads for the sample that pass QC filtering. Created if duplex basecalling is requested.",
      "mime-type": "application/x-gzip",
      "optional": true,
      "type": "per-sample"
    },    
    "simplex-alignment-pass-index": {
      "filepath": "{{ alias }}.pass.simplex.{{ format }}.{{ index_format }}",
      "title": "Simplex alignment file index of passed reads",
      "description": "The index of the resulting BAM or CRAM file with the simplex reads that pass QC filtering.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "duplex-alignment-pass-index": {
      "filepath": "{{ alias }}.pass.duplex.{{ format }}.{{ index_format }}",
      "title": "Duplex alignment file index of passed reads",
      "description": "The index of the resulting BAM or CRAM file with the duplex reads that pass QC filtering. Created if duplex basecalling is requested.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "simplex-alignment-fail": {
      "filepath": "{{ alias }}.fail.simplex.{{ format }}",
      "title": "Simplex alignment file of failed reads",
      "description": "BAM or CRAM file of simplex reads for the sample that fail QC filtering.",
      "mime-type": "application/x-gzip",
      "optional": false,
      "type": "per-sample"
    },    
    "duplex-alignment-fail": {
      "filepath": "{{ alias }}.fail.duplex.{{ format }}",
      "title": "Duplex alignment file of failed reads",
      "description": "BAM or CRAM file of duplex reads for the sample that fail QC filtering. Created if duplex basecalling is requested.",
      "mime-type": "application/x-gzip",
      "optional": true,
      "type": "per-sample"
    },    
    "simplex-alignment-fail-index": {
      "filepath": "{{ alias }}.fail.simplex.{{ format }}.{{ index_format }}",
      "title": "Simplex alignment file index of failed reads",
      "description": "The index of the resulting BAM or CRAM file with the simplex reads that fail QC filtering.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "duplex-alignment-fail-index": {
      "filepath": "{{ alias }}.fail.duplex.{{ format }}.{{ index_format }}",
      "title": "Duplex alignment file index of failed reads",
      "description": "The index of the resulting BAM or CRAM file with the duplex reads that fail QC filtering. Created if duplex basecalling is requested.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "reference-index": {
      "filepath": "{{ ref }}.fai",
      "title": "Index of the reference FASTA file",
      "description": "Index of the reference FASTA file.",
      "mime-type": "text/tab-separated-values",
      "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 reference genome.",
      "mime-type": "text/json",
      "optional": true,
      "type": "aggregated"
    }    
  }
}