ANN: NGLess v1.5.0

[Luis Pedro Coelho]

Hi everyone,

We just released version 1.5.0 of NGLess. Bioconda and docker versions are up to date.

The big change is that samples can now be specified using YAML

https://ngless.readthedocs.io/en/latest/yaml-list.html

Also, there is a new interface for parallel, namely "run_for_all/run_for_all_samples". This is a simpler (but slightly more limited) version of lock1()

Under the hood, there were a lot of changes motivated by the fact that I needed to run NGLess on over 50 thousand metagenomes and some of the way it worked before was not as robust as it should be. As usual, the tricky bits to write code for is what to do when things go wrong.

Full change log is at:

https://ngless.readthedocs.io/en/latest/whatsnew.html#version-1-5-0

HTH
Luis

Luis Pedro Coelho | Fudan University | https://luispedro.org
https://orcid.org/0000-0002-9280-7885

[juli...@free.fr]

Hi luis,

do you have an example of script that combine yaml, paired read and motus?

I tried something like

ngless "1.5"
import "samtools" version "1.0"
import "parallel" version "1.1"
local import "motus" version "2.6"

samples = load_sample_list('samples_test.yaml')
sample = lock1(samples)
input = run_for_all_samples(samples)

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

 count = motus(input,

              sample=sample,
              relative_abundance=false)

 collect(count,
          current=sample,
          allneeded=samples,

          ofile='data-raw/motus/all_samples.motusv2.tsv')

but it failed

++

Ju.