output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "wf-transcriptomes-report.html",
      "title": "workflow report",
      "description": "a HTML report document detailing the primary findings of the workflow",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "read-stats-per-file": {
      "filepath": "fastq_ingress_results/{{ alias }}//reads/fastcat_stats/per-file-stats.tsv",
      "title": "Per file read stats",
      "description": "A TSV with per file read stats, including all samples.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "aggregated"
    },
    "read-stats-per-read": {
      "filepath": "fastq_ingress_results/{{ alias }}//reads/fastcat_stats/per-read-stats.tsv",
      "title": "Read stats",
      "description": "A TSV with per read stats, including all samples.",
      "mime-type": "text/tab-separated-values",
      "optional": false,
      "type": "aggregated"
    },
    "run-ids": {
      "filepath": "fastq_ingress_results/{{ alias }}//reads/fastcat_stats/run_ids",
      "title": "Run ID's",
      "description": "List of run IDs present in reads.",
      "mime-type": "text/txt",
      "optional": false,
      "type": "aggregated"
    },
    "metamap": {
      "filepath": "fastq_ingress_results/{{ alias }}//reads/metamap.json",
      "title": "Meta map json",
      "description": "Metadata used in workflow presented in a JSON.",
      "mime-type": "text/json",
      "optional": false,
      "type": "aggregated"
    },
    "sample-data": {
      "filepath": "fastq_ingress_results/{{ alias }}//reads/{{ alias }}.fastq.gz",
      "title": "Concatenated sequence data",
      "description": "Per sample reads concatenated in to one FASTQ file.",
      "mime-type": "text/json",
      "optional": false,
      "type": "per-sample"
    },
    "transcriptome": {
      "filepath": "{{ alias }}_transcriptome.fas",
      "title": "Assembled transcriptome",
      "description": "Per sample assembled transcriptome.  Not output if a reference annotation was supplied",
      "mime-type": "text/x-fasta",
      "optional": true,
      "type": "per-sample"
    },
    "merged_transcriptome": {
      "filepath": "{{ alias }}_merged_transcriptome.fas",
      "title": "Annotated assembled transcriptome",
      "description": "Per sample annotated assembled transcriptome. Only output if a reference annotation was supplied",
      "mime-type": "text/x-fasta",
      "optional": true,
      "type": "per-sample"
    },
    "alignment-stats": {
      "filepath": "{{ alias }}_read_aln_stats.tsv",
      "title": "Alignment summary statistics",
      "description": "Per sample alignment summary statistics.",
      "mime-type": "text/tab-separated-valuesa",
      "optional": false,
      "type": "per-sample"
    },
    "gff_compare": {
      "filepath": "{{ alias }}_gffcompare",
      "title": "GFF compare results.",
      "description": "All GFF compare output files.",
      "mime-type": "text/directory",
      "optional": true,
      "type": "per-sample"
    },
    "dge-results-tsv": {
      "filepath": "de_analysis/results_dge.tsv",
      "title": "Differential gene expression results",
      "description": "This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dge-report-pdf": {
      "filepath": "de_analysis/results_dge.pdf",
      "title": "Differential gene expression report",
      "description": "Summary report of differential gene expression analysis as a PDF.",
      "mime-type": "application/pdf",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-gene-tsv": {
      "filepath": "de_analysis/results_dtu_gene.tsv",
      "title": "Differential transcript usage gene TSV",
      "description": "This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-report-pdf": {
      "filepath": "de_analysis/results_dtu.pdf",
      "title": "Differential transcript usage report",
      "description": "Summary report of differential transcript usage results as a PDF.",
      "mime-type": "application/pdf",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-transcript": {
      "filepath": "de_analysis/results_dtu_transcript.tsv",
      "title": "Differential transcript usage TSV",
      "description": "This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dtu-stageR": {
      "filepath": "de_analysis/results_dtu_stageR.tsv ",
      "title": "Differential transcript usage stageR TSV",
      "description": "This is the output from StageR and it shows both gene and transcript probabilities of differential expression",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "dexseq": {
      "filepath": "de_analysis/results_dexseq.tsv",
      "title": "Differential transcript usage DEXSeq TSV",
      "description": "The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "gene_counts": {
      "filepath": "de_analysis/all_gene_counts.tsv",
      "title": "Gene counts",
      "description": "Raw gene counts created by the Salmon tool, before filtering.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "gene_counts_per_million": {
      "filepath": "de_analysis/cpm_gene_counts.tsv",
      "title": "Gene counts per million",
      "description": "This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "transcript_counts": {
      "filepath": "de_analysis/unfiltered_transcript_counts_with_genes.tsv",
      "title": "Transcript counts",
      "description": "Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "tpm_transcript_counts": {
      "filepath": "de_analysis/unfiltered_tpm_transcript_counts.tsv",
      "title": "Transcript per million counts",
      "description": "This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "transcipt_counts_filtered": {
      "filepath": "de_analysis/filtered_transcript_counts_with_genes.tsv",
      "title": "Transcript counts filtered",
      "description": "Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "transcripts_table": {
      "filepath": "{{ alias }}_transcripts_table.tsv",
      "title": "Transcript info table",
      "description": "This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml)",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "per-sample"
    },
    "final_non_redundant_transcriptome": {
      "filepath": "de_analysis/final_non_redundant_transcriptome.fasta",
      "title": "Final non redundant transcriptome",
      "description": "Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis. Only applicable when the ref_transcriptome parameter is not provided.",
      "mime-type": "text/x-fasta",
      "optional": true,
      "type": "aggregated"
    },
    "reference-index": {
      "filepath": "igv_reference/{{ ref_genome file }}.fai",
      "title": "Index of reference FASTA file",
      "description": "Reference genome index of the FASTA file required for IGV config.",
      "mime-type": "text/tab-separated-values",
      "optional": true,
      "type": "aggregated"
    },
    "reference-gzi-index": {
        "filepath": "igv_reference/{{ ref_genome file }}.gzi",
        "title": "GZI index of the reference FASTA file",
        "description": "GZI Index of the reference FASTA file.",
        "mime-type": "application/octet-stream",
        "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.",
      "mime-type": "text/json",
      "optional": true,
      "type": "aggregated"
    },
    "minimap2-bam": {
      "filepath": "BAMS/{{ alias }}.reads_aln_sorted.bam",
      "title": "BAM file (minimap2)",
      "description": "BAM file generated from mapping input reads to the reference.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "minimap2-index": {
      "filepath": "BAMS/{{ alias }}.reads_aln_sort.bam.bai",
      "title": "BAM index file (minimap2)",
      "description": "Index file generated from mapping input reads to the reference.",
      "mime-type": "application/octet-stream",
      "optional": true,
      "type": "per-sample"
    }
  }
}