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meta.yaml
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meta.yaml
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name: emu abundance
description: Generate relative abundance estimates from ONT, Pac-Bio or short 16S reads using emu.
url: https://github.com/treangenlab/emu
authors:
- Curro Campuzano
input:
- reads: single fastq file or paired fastq files
- db: emu database (optional; check documentation for pre-built databases and how to build them).
output:
- abundances: TSV with relative (and optionally, absolute abundances).
- alignments: SAM file with the alignments (optional).
- unclassified: FASTA file with unclassified sequences (optional).
params:
extra: Any optimal parameter such as --type (sequencer) or --min-abundance. Optional flags involving output are handled automatically (e.g. --output-dir, --output-basename ...)