198 lines
7.7 KiB
JSON
198 lines
7.7 KiB
JSON
{
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"files": {
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"workflow-report": {
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"filepath": "wf-transcriptomes-report.html",
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"title": "workflow report",
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"description": "a HTML report document detailing the primary findings of the workflow",
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"mime-type": "text/html",
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"optional": false,
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"type": "aggregated"
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},
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"read-stats-per-file": {
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"filepath": "fastq_ingress_results/reads/fastcat_stats/per-file-stats.tsv",
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"title": "Per file read stats",
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"description": "A TSV with per file read stats, including all samples.",
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"mime-type": "text/tab-separated-values",
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"optional": false,
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"type": "aggregated"
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},
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"read-stats-per-read": {
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"filepath": "fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv",
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"title": "Read stats",
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"description": "A TSV with per read stats, including all samples.",
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"mime-type": "text/tab-separated-values",
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"optional": false,
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"type": "aggregated"
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},
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"run-ids": {
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"filepath": "fastq_ingress_results/reads/fastcat_stats/run_ids",
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"title": "Run ID's",
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"description": "List of run IDs present in reads.",
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"mime-type": "text/txt",
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"optional": false,
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"type": "aggregated"
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},
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"metamap": {
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"filepath": "fastq_ingress_results/reads/metamap.json",
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"title": "Meta map json",
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"description": "Metadata used in workflow presented in a JSON.",
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"mime-type": "text/json",
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"optional": false,
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"type": "aggregated"
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},
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"sample-data": {
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"filepath": "fastq_ingress_results/reads/{{ alias }}.fastq.gz",
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"title": "Concatenated sequence data",
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"description": "Per sample reads concatenated in to one FASTQ file.",
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"mime-type": "text/json",
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"optional": false,
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"type": "per-sample"
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},
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"transcriptome": {
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"filepath": "{{ alias }}_transcriptome.fas",
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"title": "Assembled transcriptome",
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"description": "Per sample assembled transcriptome.",
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"mime-type": "text/x-fasta",
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"optional": true,
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"type": "per-sample"
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},
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"merged_transcriptome": {
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"filepath": "{{ alias }}_merged_transcriptome.fas",
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"title": "Annotated assembled transcriptome",
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"description": "Per sample annotated assembled transcriptome.",
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"mime-type": "text/x-fasta",
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"optional": true,
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"type": "per-sample"
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},
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"alignment-stats": {
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"filepath": "{{ alias }}_read_aln_stats.tsv",
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"title": "Alignment summary statistics",
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"description": "Per sample alignment summary statistics.",
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"mime-type": "text/tab-separated-valuesa",
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"optional": false,
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"type": "per-sample"
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},
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"gff_compare": {
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"filepath": "{{ alias }}_gffcompare",
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"title": "GFF compare results.",
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"description": "All GFF compare output files.",
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"mime-type": "text/directory",
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"optional": true,
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"type": "per-sample"
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},
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"dge-results-tsv": {
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"filepath": "/de_analysis/results_dge.tsv",
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"title": "Differential gene expression results",
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"description": "This is a gene-level result file that describes genes and the probability that they show differential expression between experimental conditions .",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"dge-report-pdf": {
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"filepath": "/de_analysis/results_dge.pdf",
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"title": "Differential gene expression report",
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"description": "Summary report of differential gene expression analysis as a PDF.",
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"mime-type": "application/pdf",
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"optional": true,
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"type": "aggregated"
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},
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"dtu-gene-tsv": {
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"filepath": "/de_analysis/results_dtu_gene.tsv",
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"title": "Differential transcript usage gene TSV",
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"description": "This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"dtu-report-pdf": {
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"filepath": "/de_analysis/results_dtu.pdf",
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"title": "Differential transcript usage report",
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"description": "Summary report of differential transcript usage results as a PDF.",
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"mime-type": "application/pdf",
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"optional": true,
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"type": "aggregated"
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},
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"dtu-transcript": {
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"filepath": "/de_analysis/results_dtu_transcript.tsv",
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"title": "Differential transcript usage TSV",
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"description": "This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"dtu-stageR": {
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"filepath": "/de_analysis/results_dtu_stageR.tsv ",
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"title": "Differential transcript usage stageR TSV",
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"description": "This is the output from StageR and it shows both gene and transcript probabilities of differential expression",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"dexseq": {
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"filepath": "/de_analysis/results_dexseq.tsv",
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"title": "Differential transcript usage DEXSeq TSV",
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"description": "The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"gene_counts": {
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"filepath": "/de_analysis/all_gene_counts.tsv",
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"title": "Gene counts",
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"description": "Raw gene counts created by the Salmon tool, before filtering.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"transcipt_counts": {
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"filepath": "/de_analysis/all_transcript_counts.tsv",
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"title": "Transcript counts",
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"description": "Raw transcript counts created by the Salmon tool, before filtering.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"transcipt_counts_filtered": {
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"filepath": "/de_analysis/all_counts_filtered.tsv",
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"title": "Transcript counts filtered",
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"description": "Filtered transcript counts, used for DE_analysis.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"tpm_transcript_counts": {
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"filepath": "/de_analysis/de_tpm_transcript_counts.tsv",
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"title": "Transcript per million counts",
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"description": "This file shows transcript per million (TPM) of the raw counts to facilitate comparisons across sample.",
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"mime-type": "text/tab-separated-values",
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"optional": true,
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"type": "aggregated"
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},
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"final_non_redundant_transcriptome": {
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"filepath": "/de_analysis/final_non_redundant_transcriptome.fasta",
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"title": "Final non redundant transcriptome",
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"description": "Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis.",
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"mime-type": "text/x-fasta",
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"optional": true,
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"type": "aggregated"
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},
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"jaffa_fasta": {
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"filepath": "/jaffal_output_{{ alias }}/jaffa_results.fasta",
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"title": "Fusion transcript sequences",
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"description": "Fusion transcript sequences output by Jaffa.",
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"mime-type": "text/x-fasta",
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"optional": true,
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"type": "per-sample"
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},
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"jaffa_results": {
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"filepath": "/jaffal_output_{{ alias }}/jaffa_results.csv",
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"title": "Fusion transcript sequence summary file",
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"description": "Fusion transcript sequences summary file output by Jaffa.",
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"mime-type": "text/csv",
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"optional": true,
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"type": "per-sample"
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}
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}
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}
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