output_definition.json

{
  "files": {
    "workflow-alignment-stats-report": {
      "filepath": "{{ alias }}.wf-human-alignment-report.html",
      "title": "Report of the alignment statistics",
      "description": "Report summarising the results of the alignment statistics for the sample.",
      "mime-type": "text/html",
      "optional": false,
      "type": "per-sample"
    },
    "workflow-snv-report": {
      "filepath": "{{ alias }}.wf-human-snp-report.html",
      "title": "Report of the SNP workflow",
      "description": "Report summarising the results of the SNP subworkflow for the sample.",
      "mime-type": "text/html",
      "optional": true,
      "type": "per-sample"
    },
    "workflow-sv-report": {
      "filepath": "{{ alias }}.wf-human-sv-report.html",
      "title": "Report of the SV workflow",
      "description": "Report summarising the results of the SV subworkflow for the sample.",
      "mime-type": "text/html",
      "optional": true,
      "type": "per-sample"
    },
    "workflow-cnv-report": {
      "filepath": "{{ alias }}.wf-human-cnv-report.html",
      "title": "Report of the CNV workflow",
      "description": "Report summarising the results of the CNV subworkflow for the sample.",
      "mime-type": "text/html",
      "optional": true,
      "type": "per-sample"
    },
    "workflow-str-report": {
      "filepath": "{{ alias }}.wf-human-str-report.html",
      "title": "Report of the STR workflow",
      "description": "Report summarising the results of the short tandem repeat subworkflow for the sample.",
      "mime-type": "text/html",
      "optional": true,
      "type": "per-sample"
    },
    "snp-vcf": {
      "filepath": "{{ alias }}.wf_snp.vcf.gz",
      "title": "Short variant VCF",
      "description": "VCF file with the SNPs for the sample.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "sv-vcf": {
      "filepath": "{{ alias }}.wf_sv.vcf.gz",
      "title": "Structural variant VCF",
      "description": "VCF file with the SVs for the sample.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "phased-vcf": {
      "filepath": "{{ alias }}.wf_human_variation.phased.vcf.gz",
      "title": "SNP and SV phased VCF",
      "description": "VCF file with the jointly phased SNPs and SVs for the sample.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "cnv-vcf": {
      "filepath": "{{ alias }}.wf_cnv.vcf.gz",
      "title": "Copy number variants VCF",
      "description": "VCF file with the CNV for the sample.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "mod-bedmethyl": {
      "filepath": "{{ alias }}.wf_mods.bedmethyl.gz",
      "title": "Modified bases BEDMethyl",
      "description": "BED file with the aggregated modification counts for the sample.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "str-vcf": {
      "filepath": "{{ alias }}.wf_str.vcf.gz",
      "title": "Short tandem repeat VCF",
      "description": "VCF file with the STR sites for the sample.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "alignment": {
      "filepath": "{{ alias }}.cram",
      "title": "Alignment file",
      "description": "CRAM or BAM file with the aligned reads for the sample, generated when the input file is unaligned.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },    
    "alignment-index": {
      "filepath": "{{ alias }}.cram.crai",
      "title": "Alignment file index",
      "description": "The index of the resulting CRAM or BAM file with the reads for the sample, generated when the input file is unaligned.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "haplotagged-alignment": {
      "filepath": "{{ alias }}.haplotagged.cram",
      "title": "Haplotagged alignment file",
      "description": "CRAM or BAM file with the haplotagged reads for the sample.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },    
    "haplotagged-alignment-index": {
      "filepath": "{{ alias }}.haplotagged.cram.crai",
      "title": "Haplotagged alignment file index",
      "description": "The index of the resulting CRAM or BAM file with the haplotagged reads for the sample.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "coverage-by-region": {
      "filepath": "{{ alias }}.regions.bed.gz",
      "title": "Mean coverage for each region",
      "description": "The mean coverage in the individual regions of the genome in BED format.",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "coverage-by-threshold": {
      "filepath": "{{ alias }}.thresholds.bed.gz",
      "title": "Coverage per region above the given thresholds",
      "description": "The BED reporting the number of bases in each region that are covered at or above each threshold values (1x, 10x, 20x and 30x).",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "distribution-of-coverage": {
      "filepath": "{{ alias }}.mosdepth.global.dist.txt",
      "title": "Distribution of the proportion of total bases covered by a given coverage value",
      "description": "The cumulative distribution indicating the proportion of total bases covered by a given coverage value, both genome-wide and by sequence.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "coverage-summary": {
      "filepath": "{{ alias }}.mosdepth.summary.txt",
      "title": "Mean coverage per sequence and target region",
      "description": "The summary of mean depths per chromosome and within specified regions per chromosome.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "coverage-per-base": {
      "filepath": "{{ alias }}.per-base.bedgraph.gz",
      "title": "BEDgraph of the single-base coverage",
      "description": "The single-base coverage of the genome in BED graph format.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    }
  }
}