{
  "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"
    },
    "read-stats-per-file": {
      "filepath": "ingress_results/{{ alias }}/fastcat_stats/per-file-stats.tsv",
      "title": "Per-file read stats",
      "description": "Read statistics for each input FASTQ file in a sample, when FASTQ read stats are available.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "per-sample"
    },
    "read-stats-per-read": {
      "filepath": "ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz",
      "title": "Per-read stats",
      "description": "Read statistics for individual reads in a sample, when this output is enabled.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "sample-fastq": {
      "filepath": "ingress_results/{{ alias }}/seqs.fastq.gz",
      "title": "Ingress reads",
      "description": "Reads prepared from the input data for downstream analysis.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "sample-metadata": {
      "filepath": "ingress_results/{{ alias }}/metamap.json",
      "title": "Ingress metadata",
      "description": "Per-sample metadata used by the workflow.",
      "mime-type": "application/json",
      "optional": true,
      "type": "per-sample"
    },
    "sample-bam": {
      "filepath": "cohort/alignments/{{ alias }}.aligned.sorted.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": "cohort/alignments/{{ alias }}.aligned.sorted.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": "cohort/alignments/{{ alias }}.flagstat.txt",
      "title": "Alignment summary",
      "description": "samtools flagstat output for the aligned BAM.",
      "mime-type": "text/plain",
      "optional": false,
      "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_cohort/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 }}/{{ 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"
    },
    "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"
    }
  }
}