{
  "files": {
    "workflow-report": {
      "filepath": "wf-transcriptomes-report.html",
      "title": "Workflow report",
      "description": "HTML report summarising transcript discovery, quantification, optional SQANTI3 classification, and optional differential analysis results.",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "sample-bam": {
      "filepath": "samples/{{ alias }}/alignment/reads.bam",
      "title": "Aligned BAM",
      "description": "Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV.",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "sample-bai": {
      "filepath": "samples/{{ alias }}/alignment/reads.bam.bai",
      "title": "Aligned BAM index",
      "description": "Index for the aligned BAM.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "sample-flagstat": {
      "filepath": "samples/{{ alias }}/alignment/bamstats.flagstat.tsv",
      "title": "Alignment summary",
      "description": "bamstats flagstat summary for the aligned BAM.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "sample-bedmethyl": {
      "filepath": "samples/{{ alias }}/mods/{{ alias }}.mods.bedmethyl.gz",
      "title": "Modified base pileup",
      "description": "Per-sample modkit bedMethyl pileup generated from the aligned BAM when MM and ML tags are present.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "sample-mod-summary": {
      "filepath": "samples/{{ alias }}/mods/{{ alias }}.mods.summary.tsv",
      "title": "Modified base summary",
      "description": "Per-sample global modification-percent summary aggregated from the modkit bedMethyl pileup, with one row per modification code.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "per-sample"
    },
    "sample-mod-bigwig": {
      "filepath": "samples/{{ alias }}/mods/{{ alias }}.mods.*.bw",
      "title": "Modified base bigWig",
      "description": "Per-sample modkit bigWig tracks generated from the aligned BAM, with one file per requested or inferred modification code.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    },
    "annotation-reference-summary": {
      "filepath": "cohort/reference/annotation_reference_summary.json",
      "title": "Reference and annotation preparation summary",
      "description": "Summary of reference and annotation preparation, including seqname overlap, build/provider hints, and excluded unstranded annotation counts.",
      "mime-type": "application/json",
      "optional": false,
      "type": "aggregated"
    },
    "unstranded-annotation": {
      "filepath": "cohort/reference/unstranded_annotation.gtf",
      "title": "Excluded unstranded annotation records",
      "description": "Full set of annotation records excluded because their strand was not '+' or '-'. Present only when unstranded records are found.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "aggregated"
    },
    "cohort-gtf": {
      "filepath": "cohort/transcripts.gtf",
      "title": "Cohort transcriptome GTF",
      "description": "Joint bambu transcript model used as the primary cohort transcriptome.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "aggregated"
    },
    "cohort-fasta": {
      "filepath": "cohort/cohort.transcriptome.fa",
      "title": "Cohort transcriptome FASTA",
      "description": "Transcript sequences derived from the joint cohort GTF.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "aggregated"
    },
    "cohort-transcript-counts": {
      "filepath": "cohort/transcript_counts.tsv",
      "title": "Cohort transcript counts",
      "description": "Transcript-level count matrix produced by bambu.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "aggregated"
    },
    "cohort-gene-counts": {
      "filepath": "cohort/gene_counts.tsv",
      "title": "Cohort gene counts",
      "description": "Gene-level count matrix derived from bambu output.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "aggregated"
    },
    "cohort-transcript-metadata": {
      "filepath": "cohort/transcript_metadata.tsv",
      "title": "Cohort transcript metadata",
      "description": "Transcript annotations and bambu transcript classes for the cohort model.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "aggregated"
    },
    "cohort-sqanti-summary": {
      "filepath": "cohort/sqanti/classification_summary.tsv",
      "title": "Cohort SQANTI3 summary",
      "description": "SQANTI3 classification summary for the cohort transcriptome when SQANTI3 QC is enabled.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "sample-gtf": {
      "filepath": "samples/{{ alias }}/transcripts.gtf",
      "title": "Per-sample transcriptome GTF",
      "description": "Independent bambu transcript model for an individual sample.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "sample-fasta": {
      "filepath": "samples/{{ alias }}/{{ alias }}.transcriptome.fa",
      "title": "Per-sample transcriptome FASTA",
      "description": "Transcript sequences derived from the per-sample GTF.",
      "mime-type": "text/plain",
      "optional": false,
      "type": "per-sample"
    },
    "sample-transcript-counts": {
      "filepath": "samples/{{ alias }}/transcript_counts.tsv",
      "title": "Per-sample transcript counts",
      "description": "Transcript-level abundance estimates for the per-sample bambu model.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "sample-gene-counts": {
      "filepath": "samples/{{ alias }}/gene_counts.tsv",
      "title": "Per-sample gene counts",
      "description": "Gene-level abundance estimates for the per-sample bambu model.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "sample-transcript-metadata": {
      "filepath": "samples/{{ alias }}/transcript_metadata.tsv",
      "title": "Per-sample transcript metadata",
      "description": "Transcript annotations and bambu transcript classes for the per-sample model.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "per-sample"
    },
    "sample-sqanti-summary": {
      "filepath": "samples/{{ alias }}/sqanti/classification_summary.tsv",
      "title": "Per-sample SQANTI3 summary",
      "description": "SQANTI3 classification summary for the per-sample transcriptome when SQANTI3 QC is enabled.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "per-sample"
    },
    "dge-results": {
      "filepath": "de_analysis/{{ contrast }}/results_dge.tsv",
      "title": "Differential gene expression results",
      "description": "DESeq2 gene-level differential expression results for one contrast.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dge-report": {
      "filepath": "de_analysis/{{ contrast }}/results_dge.pdf",
      "title": "Differential gene expression plots",
      "description": "PDF plots generated during DESeq2 analysis for one contrast.",
      "mime-type": "application/pdf",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-transcript-results": {
      "filepath": "de_analysis/{{ contrast }}/results_dtu_transcript.tsv",
      "title": "Differential transcript usage results",
      "description": "Transcript-level DTU results for one contrast.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-gene-results": {
      "filepath": "de_analysis/{{ contrast }}/results_dtu_gene.tsv",
      "title": "Differential transcript usage gene summary",
      "description": "Gene-level DTU summary for one contrast.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dexseq-results": {
      "filepath": "de_analysis/{{ contrast }}/results_dexseq.tsv",
      "title": "DEXSeq results",
      "description": "Full DEXSeq result table for one contrast.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-report": {
      "filepath": "de_analysis/{{ contrast }}/results_dtu.pdf",
      "title": "Differential transcript usage plots",
      "description": "PDF plots generated during DEXSeq analysis for one contrast.",
      "mime-type": "application/pdf",
      "optional": true,
      "type": "aggregated"
    },
    "de-qc-stats": {
      "filepath": "de_analysis/de_qc_stats.json",
      "title": "Differential analysis QC summary",
      "description": "Structured DE/DTU QC summary. Use analysis_fallbacks for aggregate counts, and each contrast's deseq2_dispersion_fallback, dexseq_dispersion_method, and dexseq_covariates_dropped fields for interpretation.",
      "mime-type": "application/json",
      "optional": true,
      "type": "aggregated"
    },
    "de-overall-summary": {
      "filepath": "de_analysis/de_overall_summary.txt",
      "title": "Differential analysis text summary",
      "description": "Human-readable DE/DTU run summary across all contrasts.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "aggregated"
    },
    "de-contrast-qc-summary": {
      "filepath": "de_analysis/{{ contrast }}/contrast_qc_summary.txt",
      "title": "Per-contrast QC summary",
      "description": "Human-readable per-contrast DE/DTU QC summary including sample counts and key significance totals.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "aggregated"
    },
    "deseq2-dispersion-fallback-diagnostic": {
      "filepath": "de_analysis/DESeq2_dispersion_fallback_{{ contrast }}.txt",
      "title": "DESeq2 fallback diagnostic",
      "description": "Diagnostic details when DESeq2 falls back to gene-wise dispersion estimation.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-analysis-failed-diagnostic": {
      "filepath": "de_analysis/{{ contrast }}/DTU_ANALYSIS_FAILED.txt",
      "title": "DTU failure diagnostic",
      "description": "Diagnostic details when DEXSeq fails for a contrast.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "aggregated"
    },
    "multiple-testing-warning": {
      "filepath": "de_analysis/MULTIPLE_TESTING_WARNING.txt",
      "title": "Multiple-testing warning",
      "description": "Family-wise error-rate note generated when multiple contrasts are tested.",
      "mime-type": "text/plain",
      "optional": true,
      "type": "aggregated"
    },
    "igv-config": {
      "filepath": "igv.json",
      "title": "IGV configuration",
      "description": "JSON configuration for viewing the aligned BAMs in IGV.",
      "mime-type": "text/json",
      "optional": true,
      "type": "aggregated"
    },
    "reference-index": {
      "filepath": "igv_reference/{{ ref_genome_file }}.fai",
      "title": "Reference FASTA index",
      "description": "FAI index for the reference genome published for IGV.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "reference-gzi-index": {
      "filepath": "igv_reference/{{ ref_genome_file }}.gzi",
      "title": "Reference GZI index",
      "description": "GZI index for a compressed reference genome published for IGV.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "aggregated"
    }
  }
}