A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

BBTools modules users... in particular BBMAP_BBDUK  - have you seen this before?

<https://github.com/nf-core/taxprofiler/issues/632>

In bbmap/bbnorm, I use `floor()` to make sure I get an integer that is lower than the maximum after multiplying with a decimal value:
```memory = "-Xmx${Math.round(Math.max(1, Math.floor(task.memory.toGiga() * 0.95)))}g"```
(This is where `ext.args.mem_multiplier` would fit in, instead of the hardcoded 0.95.)

I'm a little puzzled over the `Math.round()` -- don't remember what that's for.

&gt; BBMAP :shakefist:
But why? If we have an issue with setting the Java memory corretly the module, it is hardly BBMAPs fault - other than maybe that it is written in Java. :tux-sorry::java:

But yes, I remember we <https://github.com/nf-core/modules/blob/master/modules/nf-core/umicollapse/main.nf|had similar issues with the umicollapse> module, so it could potentially be handled like there. The `bbnorm` solution also looks good.

It is the modules/java fault, but I have had other issues with BBtool which makes me also :shakefist:

<https://github.com/nf-core/modules/pull/8938>

should we check all modules with such memory requirement?

OK that's just an easy/obvious/riught in your face fix :facepalm:  thank you <@UNMC49PJS>!

seems several of the bbmap modules need it, but we should also choose a fixed way for all the modules. There are at least 3 different memory setting implementations

I'll at least merge this into taxprofiler and get the reporter to confirm that it satisfies them

<https://github.com/nf-core/taxprofiler/pull/635>

Any chance someone can review so I can ask  the reporter to test?

Does that warrant an advisory or is the fact, that <https://github.githistory.xyz/nf-core/modules/blob/master/modules/nf-core/bbmap/bbduk/main.nf|it didn’t cause any harm in the past 3 years> an indication that very few people specify the task memory in MB?

The module is used in several pipelines, <https://nf-co.re/modules/bbmap_bbduk/|so that would mean lots of  affected releases>…

I actually wondered that too, but like you said, specifying in MB seems _very_ rare

And I don't think it's a silent fail which is maybe where advisories is more important

Fair enough. I am certainly not keen on gathering all releases with that module :see_no_evil: