Samples are defined with a name, file path(s) and the type of data. A single file path is interpreted as interleaved paired-end reads or single-end, while two paths must include full paths to R1 and R2.
Sample names must be unique and not contain spaces or underscores (dashes are accepted).
type, the value can be either ‘metagenome’ or ‘metatranscriptome’. If
neither is specified, the default is ‘metagenome’.
A single file path is specified for
also being set. In this case,
paired are optional as we are
using the values that are equal to the defaults.
samples: sample-1: fastq: /data/sample-1_pe.fastq.gz type: metagenome paired: true
In this case, we create a list using YAML syntax for both R1 and R2 indexes:
samples: sample-1: fastq: - /data/sample-1_R1.fastq.gz - /data/sample-1_R2.fastq.gz type: metagenome paired: true
The ‘-‘ is required if multiple fastq file paths need to be specified.
Data is assumed to be paired-end unless stated otherwise. If your data is
single-end sequence data, specify
samples: sample-1: fastq: /data/sample-1_pe.fastq.gz type: metagenome paired: false