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output_definition.json
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output_definition.json
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{
"files": {
"workflow-report": {
"filepath": "wf-metagenomics-report.html",
"title": "workflow report",
"description": "Report for all samples.",
"mime-type": "text/html",
"optional": false,
"type": "aggregated"
},
"abundance-table-rank": {
"filepath": "abundance_table_{{ taxonomic_rank }}.tsv",
"title": "Abundance table with counts per taxa",
"description": "Per-taxa counts TSV, including all samples.",
"mime-type": "text/tab-separated-values",
"optional": false,
"type": "aggregated"
},
"bracken-report": {
"filepath": "bracken/{{ alias }}.kraken2_bracken.report",
"title": "Bracken report file",
"description": "TSV file with the abundance of each taxa. More info about [bracken report](https://github.com/jenniferlu717/Bracken#output-kraken-style-bracken-report).",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
},
"kraken-report": {
"filepath": "kraken2/{{ alias }}.kraken2.report.txt",
"title": "Kraken2 taxonomic assignment per read (Kraken2 pipeline)",
"description": "Lineage-aggregated counts. More info about [kraken2 report](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#sample-report-output-format).",
"mime-type": "text/txt",
"optional": true,
"type": "per-sample"
},
"kraken-assignments": {
"filepath": "kraken2/{{ alias }}.kraken2.assignments.tsv",
"title": "Kraken2 taxonomic asignment per read (Kraken2 pipeline)",
"description": "TSV file with the taxonomic assignment per read. More info about [kraken2 assignments report](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#standard-kraken-output-format).",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
},
"host-bam": {
"filepath": "host_bam/{{ alias }}.bam",
"title": "Host BAM file",
"description": "BAM file generated from mapping filtered input reads to the host reference.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"host-bai": {
"filepath": "host_bam/{{ alias }}.bai",
"title": "BAM index file of host reads",
"description": "BAM index file generated from mapping filtered input reads to the host reference.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"minimap2-bam": {
"filepath": "bams/{{ alias }}.reference.bam",
"title": "BAM file (minimap2)",
"description": "BAM file generated from mapping filtered input reads to the reference.",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"minimap2-index": {
"filepath": "bams/{{ alias }}.reference.bam.bai",
"title": "BAM index file (minimap2)",
"description": "Index file generated from mapping filtered input reads to the reference.",
"mime-type": "application/octet-stream",
"optional": true,
"type": "per-sample"
},
"minimap2-flagstats": {
"filepath": "bams/{{ alias }}.bamstats_results/bamstats.flagstat.tsv",
"title": "BAM flagstat (minimap2)",
"description": "Mapping results per reference",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
},
"minimap2-bamreadstats": {
"filepath": "bams/{{ alias }}.bamstats_results/bamstats.readstats.tsv.gz",
"title": "Minimap2 alignment statistics (minimap2)",
"description": "Per read stats after aligning",
"mime-type": "application/gzip",
"optional": true,
"type": "per-sample"
},
"amr-report": {
"filepath": "amr/{{ alias }}.json",
"title": "JSON file with identified AMR genes (amr)",
"description": "JSON file with abricate results. More info about [abricate output](https://github.com/tseemann/abricate#output).",
"mime-type": "text/json",
"optional": true,
"type": "per-sample"
},
"reduced-reference": {
"filepath": "igv_reference/reduced_reference.fasta.gz",
"title": "Reduced reference FASTA file",
"description": "Reference FASTA file containing only those sequences that have reads mapped against them.",
"mime-type": "application/gzip",
"optional": true,
"type": "aggregated"
},
"reduced-reference-index": {
"filepath": "igv_reference/reduced_reference.fasta.gz.fai",
"title": "Index of the reduced reference FASTA file",
"description": "Index of the reference FASTA file containing only those sequences that have reads mapped against them.",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "aggregated"
},
"reduced-reference-gzi-index": {
"filepath": "igv_reference/reduced_reference.fasta.gz.gzi",
"title": "GZI index of the reduced reference FASTA file",
"description": "Index of the reference FASTA file containing only those sequences that have reads mapped against them.",
"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 reduced reference.",
"mime-type": "text/json",
"optional": true,
"type": "aggregated"
},
"read-assignments": {
"filepath": "reads_assignments/{{ alias }}.*.assignments.tsv",
"title": "Taxonomic assignment per read.",
"description": "TSV file with the taxonomic assignment per read.",
"mime-type": "text/tab-separated-values",
"optional": true,
"type": "per-sample"
},
"extracted-fastq": {
"filepath": "extracted/{{ alias }}.minimap2.extracted.fastq",
"title": "FASTQ of the selected taxids.",
"description": "FASTQ containing/excluding the reads of the selected taxids.",
"mime-type": "text",
"optional": true,
"type": "per-sample"
}
}
}