Defining Samples

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).

For type, the value can be either ‘metagenome’ or ‘metatranscriptome’. If neither is specified, the default is ‘metagenome’.

Interleaved Input

A single file path is specified for fastq with type and paired also being set. In this case, type and 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

Paired-end Input

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.

Single-end Input

Data is assumed to be paired-end unless stated otherwise. If your data is single-end sequence data, specify paired as false:

samples:
    sample-1:
        fastq: /data/sample-1_pe.fastq.gz
        type: metagenome
        paired: false