output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "./wf-amplicon-report.html",
      "title": "workflow report",
      "description": "Report for all samples.",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "sanitized-ref": {
      "filepath": "./reference_sanitized_seqIDs.fasta",
      "title": "Sanitized reference file",
      "description": "Some programs used by the workflow don't like special characters (like colons) in the sequence IDs in the reference FASTA file. The reference is thus \"sanitized\" by replacing these characters with underscores. This file is only generated when the workflow is run in variant calling mode.",
      "mime-type": "text/txt",
      "optional": true,
      "type": "aggregated"
    },
    "sanitized-ref-index": {
      "filepath": "./reference_sanitized_seqIDs.fasta.fai",
      "title": "Sanitized reference index file",
      "description": "FAI index for the sanitised reference FASTA file.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "alignments": {
      "filepath": "./{{ alias }}/alignments/{{ alias }}.aligned.sorted.bam",
      "title": "Alignments BAM file",
      "description": "BAM file with alignments of input reads against the references (in variant calling mode) or the created consensus (in de-novo consensus mode).",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "alignments-index": {
      "filepath": "./{{ alias }}/alignments/{{ alias }}.aligned.sorted.bam.bai",
      "title": "Alignments index file",
      "description": "Index for alignments BAM file.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "consensus-fastq": {
      "filepath": "./{{ alias }}/consensus/consensus.fastq",
      "title": "De-novo consensus FASTQ file",
      "description": "Consensus sequence file generated by de-novo consensus pipeline.",
      "mime-type": "text/txt",
      "optional": true,
      "type": "per-sample"
    },
    "consensus-fasta": {
      "filepath": "./{{ alias }}/consensus/medaka.consensus.fasta",
      "title": "Consensus FASTA file",
      "description": "Consensus sequence file generated by variant calling pipeline.",
      "mime-type": "text/txt",
      "optional": true,
      "type": "per-sample"
    },
    "variants": {
      "filepath": "./{{ alias }}/variants/medaka.annotated.vcf.gz",
      "title": "Variants VCF file",
      "description": "VCF file of variants detected against the provided reference.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "variants-index": {
      "filepath": "./{{ alias }}/variants/medaka.annotated.vcf.gz.csi",
      "title": "Variants index file",
      "description": "Index for variants VCF file.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "all-de-novo-consensus-seqs": {
      "filepath": "./all-consensus-seqs.fasta",
      "title": "Combined de-novo consensus sequences",
      "description": "FASTA file containing all de-novo consensus sequences.",
      "mime-type": "text/txt",
      "optional": true,
      "type": "aggregated"
    },
    "all-de-novo-consensus-seqs-index": {
      "filepath": "./all-consensus-seqs.fasta.fai",
      "title": "Combined de-novo consensus sequences index",
      "description": "FAI index for the FASTA file with the combined de-novo consensus sequences.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "igv-config": {
      "filepath": "./igv.json",
      "title": "IGV config JSON file",
      "description": "JSON file with IGV config options to be used by the EPI2ME Desktop Application.",
      "mime-type": "application/json",
      "optional": true,
      "type": "aggregated"
    }
  }
}