ngless-toolkit/ng-meta-profiler

Profiler for metagenomics based on NGLess

ng-meta-profiler's Issues

Make the mOTUs 2 human profiler the main one

The recommendation should be to use the state-of-the-art.

om-rgc module version mismatch

In

ng-meta-profiler/marine-profiler.ngl

Line 4 in 4b7b49a

import "om-rgc" version "0.9"

we refer om-rgc 0.9 but we only have om-rgc 0.0.
Should we a) create the 0.9 module or instead b) downgrade the ngless script to 0.0.

Since we also have the ng-meta-profiler scripts on Zenodo, if we go for b) we will need to update those as well.

Profiler for Soil metagenomes

Hello @luispedro @unode

What's the recommendation when dealing with soil metagenomes since there is no particular predefined profiler for it or any other metagenome that has no predefined profiler for that matter?

temporary directory not working

Hi,
I am running the pipeline in an slurm enviroment and even though I specified the -t to write into scratch, the pipeline start to write on ~/.local/share/ngless (specifically /users/valensan/.local/share/ngless/data.tar.gz2776146-0.tmp). Which at some point runs out of disk space.

error log:

Exiting after fatal error:
An unhandled error occurred (this should not happen)!

	If you can reproduce this issue, please run your script
	with the --trace flag and report a bug (including the script and the trace) at
		https://github.com/ngless-toolkit/ngless/issues

The error message was: `/users/valensan/.local/share/ngless/data/Modules/igc.ngm/0.9/igc.fna: hPutBuf: permission denied (Quota exceeded)`

I tried also by exporting another temporary path but didn't work.

what could I do?
thanks in advance!