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Hi! I am new to using an nf-core pipeline on PDC, ...
# helpdesk-hpc-sweden
k
Hi! I am new to using an nf-core pipeline on PDC, mores specifically nf-core/pangenome. I tried to use the pdc_kth config file but run into some problems, which seems to have to do with Nexflow itself. I tried to use the nextflow/26.04.3 module, would you say it's preferable to download nextflow instead and put it into bin?
p
That doesn't really matter I think. It seems pangenome doesn't like a new nextflow, running with 
NXF_VER=25.10.4 NXF_SYNTAX_PARSER=v1
prepended seems to work better.
k
thanks! in the script, in the config file or in the params file?
p
In your launch script (prepended 
A=B
is a quick way to run a command with the environment variable 
A
set to 
B
for just that command, for the nextflow launch script this can be used to choose what actual nextflow version is used).
Since it affects so basic things, it can't be done within nextflow.
If you think it's clearer,
Copy code
NXF_VER=25.10.4
export NXF_VER
NXF_SYNTAX_PARSER=v1
export NXF_SYNTAX_PARSER
is close enough to the same thing.
k
Get it!
Thanks a lot, now it's running as it should, I think 😅
+ I loaded singularity module now but saw that there is an apptainer module mentioned in the config file. Should I then skip loading "my" module?
p
No, you need to have the module loaded in your launch script for the monitoring process to be able to download container images.
For the actual jobs, the apptainer module will be loaded to run them.
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