YAML input count & collect

[ullo...@googlemail.com]

Dear all,

I have a question regarding the YAML input format, what do I put into the collect function for the allneeded parameter? Here is an example:

ngless "1.5"

local import "motus" version "3.1"

import "parallel" version "1.1"

samples=load_sample_list('all_samples.yaml')

input = run_for_all_samples(samples)

count = motus(input,

              sample=input.name(),

              relative_abundance=false)

collect(count,

   current=input.name(),

        allneeded=samples,

        ofile='project_motusv3.1.tsv')

Are "sample" and "current" correctly defined? at least it does not throw an error validating the script.

Yours sincerely,

Ulrike

[Luis Pedro Coelho]

Sorry for the late reply, moving continents was a big disruption.

To me this seems good, yes.

HTH, Luis

--

You received this message because you are subscribed to the Google Groups "NGLess" group.

To unsubscribe from this group and stop receiving emails from it, send an email to ngless+un...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/ngless/21ba4fa0-466e-411f-9cff-ee8f79222219n%40googlegroups.com.

[Ulrike Löber]

Dear Luis,

But allneeded is not correctly defined. It does not run. Please help.

Yours sincerely,

Ulrike

Gesendet von Yahoo Mail auf Android

Am Fr., Okt. 6, 2023 at 7:22 schrieb Luis Pedro Coelho

<lu...@luispedro.org>:

[Luis Pedro Coelho]

Sorry that was way too quick

I think the answer is that you leave them out:

collect(count,

    ofile='project_motusv3.1.tsv')

The run_for_all_samples will magically fill it in correctly

HTH, Luis

Luis Pedro Coelho | Queensland University of Technology | https://luispedro.org

https://orcid.org/0000-0002-9280-7885