YAML based sample lists

Since NGLess 1.5

Specifying a list of samples in a YAML file:

You can specify a list of samples in YAML format.

basedir: /share/data/metagenomes
samples:
  sample1:
    - paired:
        - data/Sample1a.1.fq.gz
        - data/Sample1a.2.fq.gz
    - paired:
        - data/Sample1b.1.fq.gz
        - data/Sample1b.2.fq.gz
  sample2:
    - paired:
        - data/Sample2.1.fq.gz
        - data/Sample2.2.fq.gz
    - single:
        - data/Sample2.extra.fq.gz

The format is the following

• basedir (optional): if specified, all relative paths are relative to this directory. Otherwise, paths are relative to the current directory where NGLess is executing (not where the YAML file is located)
• samples: a dictionary mapping a sample name to a list of files

Using the YAML format in NGLess

You can load a sample list with the load_sample_list function:

ngless "1.5"
samples = load_sample_list('list.yaml')
input = samples[0]

input = preprocess(input) using |read|:
    read = substrim(read, min_quality=25)
    if len(read) < 45:
        discard
...

It can also be used with the parallel module module’s run_for_all_samples function. For example:

ngless "1.5"
import "parallel" version "1.1"
input = run_for_all_samples(load_sample_list('list.yaml'))

input = preprocess(input) using |read|:
    read = substrim(read, min_quality=25)
    if len(read) < 45:
        discard

write(input, ofile='outputs' </> input.name() + '.fq.xz')
...

Note how we used the .name() method in the readset object to get the name of the selected sample.

Loading a single sample from an YAML file

The function load_sample_from_yaml (which takes a YAML file and a mandatory sample argument) will return a single sample (identified by the sample argument).

ngless "1.5"
input = load_sample_from_yaml('list.yaml', sample='sample-id')
...