Closed ropolomx closed 3 years ago
Hi!
The issue you mentioned, https://github.com/nf-core/fetchngs/issues/12, seems to me rather because of a wrong choice of container in the pipeline script. The fix was to use another container. However, it seems to me that your problem isn't related.
To me, your issue seems to be related to https://github.com/nf-core/eager/issues/68, i.e. it might be a config problem.
But I admit that I am not an expert in that matter. I will use the pipeline in the next days, and if its a container problem I will run into it too (and fix it).
If you do want to test the potential config solution, please let me know in case that works, otherwise I think I have to refer you to the nf-core slack with more knowledgeable people for that problem.
Best
Hi @d4straub ! Thank you so much for pointing me to the issue of the eager
repo. Indeed this was a config problem, and I fixed this with the following in my config file. We don't have module
in our cluster, and we are encouraged to use conda
to activate the singularity
env. This seems to work. Thank you for taking the time to look into this and replying to me!
process {
executor = 'sge'
clusterOptions = '-cwd -V'
penv = 'smp'
beforeScript = 'source ~/miniconda3/etc/profile.d/conda.sh; conda activate singularity'
}
Check Documentation
I have checked the following places for your error:
Description of the bug
Command:
nextflow run nf-core/mag -r 2.1.0 -profile test,singularity -c sge.conf
Error:
sge.conf:
Steps to reproduce
Steps to reproduce the behaviour:
Expected behaviour
Pipeline would launch jobs with the
sge
executor using Singularity images.Log files
Have you provided the following extra information/files:
.nextflow.log
fileSystem
Nextflow Installation
Container engine
Additional context
This issue might be similar to this other issue in
fetchngs
I do have a Singularity cache directory where those containers were already downloaded