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```Hello, I am trying to run the nf-core/demo on a...
# nostupidquestions
s
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Hello, I am trying to run the nf-core/demo on a cluster before I run the ampliseq pipeline, and I must have a syntax error somewhere. I am using the code given on the webpage: nextflow run nf-core/demo -profile test,docker --outdir results                                                                                                                                                    My cluster has nextflow 24.06.4. I am getting errors with this code. I have tried placing a space after the comma, and I have tried no comma. I have also tried not including the comma or docker after test. The pipeline does not complete and gives error code 127. In one of those scenarios, I get a hint : "A common mistake is to provide multiple values separated by spaces e.g. 'profile test, docker'. I am not sure how to fix my syntax. I am also new to nf-core, containers and pipelines. I have been reading the troubleshooting guide, but I am not seeing a solution to this error. Thank you!
m
hi, what is the exact log you get when running 
nextflow run nf-core/demo -profile test,docker --outdir results
?
(be aware nf-core/demo has a minimum nextflow version of 25.10.4, so one possible reason is that your version is not supported anymore)
s
That is helpful to know, but the 24 was a typo. It has nextflow 26.04.4.
👍🏻 1
m
looks like you docker is not running, is that possible?
also on clusters people usually use singularity/apptainer. maybe that's what you need here?
s
Yes, but I do not know how to fix that. Do I need to call or load it before?
m
what cluster are you using? maybe we have a config for it already in https://nf-co.re/configs/
s
I think I tried singularity, but I can try again. I have not tried apptainer yet.
s
apptainer generally comes with a replacement that makes 
singularity
actually call 
apptainer
instead
s
I am using the cluster from Institut Francais de Bioinformatique (IFB).
m
https://nf-co.re/configs/ifb_core/ maybe this is helpful then?
s
try 
which singularity
and 
which apptainer
to see if either returns a hit. Some clusters you have to load singularity with a 
lmod
or 
module load
command
yeah, looks like IFB you need to use 
module load
. But that is what the magic of the configs is for
spiderman pointing 1
m
module load singularity
according to the config docs linked above
s
Thank you both! I will look into this!
👍🏻 1
s
(although it looks like that config doesn't automatically load singularity on the worker nodes...)
Some other cluster configs have 
process.beforeScript   = 'module load singularity'
, which will do that
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