237 lines
9.8 KiB
JSON
237 lines
9.8 KiB
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"
|
|
}
|
|
}
|
|
}
|