New module: xengsort

[vladsavelyev]

Fix #2165

[github-actions]

🚀 Deployed on https://mqc-pr-2168--multiqc.netlify.app

[tamuanand]

Hi @vladsavelyev

The help text for the actual xengsort classify command at https://mqc-pr-2168--multiqc.netlify.app/modules/xengsort/ should be changed - --method count should actually be --classification count such that it looks like

xengsort classify --index myindex \
  --fastq paired.1.fq.gz --pairs paired.2.fq.gz \
 --prefix myresults \
  --classification count \
 > sample.txt

I am guessing you probably grabbed that help text from their gitlab page

• https://gitlab.com/genomeinformatics/xengsort#how-to-classify
• which states --method count
• and that is incorrect - it should be --classification count

I have submitted an issue on their gitlab - https://gitlab.com/genomeinformatics/xengsort/-/issues/36#note_1638925835

I believe the docs here are incorrect - https://gitlab.com/genomeinformatics/xengsort#how-to-classify

it has it as --method count and I believe this should be --classification count based on CLI help using xengsort 2.0.1

[Jens Zentgraf](https://gitlab.com/jens.zentgraf)
[@jens.zentgraf](https://gitlab.com/jens.zentgraf)
Maintainer
Hi, thanks for pointing this out. I will update the README. Best Jens

[tamuanand]

Great job @vladsavelyev

Some other suggestions:- Just like with xenome at #2164, for xengsort it would be great to have

• a summary table in addition to the general stats column and hidden columns for read counts.
• section wrappers to the plots to make sure they appear in the contents panel.

Thanks

[tamuanand]

I would suggest that xengsort summary stats table should be consistent with xenome summary stats table

• hence, it would be better to have graft reads as column 1 (Human reads in xenome) and host reads as column 2 (Mouse reads in xenome)

[ewels]

LGTM!

[ewels]

This doesn't seem to be the case.

Suggested change

	Then the sample name in the report will be `sample`, which is the base name of the file.