Bug in the nextflow.config

[tinahuang222]

Hi,

When I tried to rerun your code in bash,
nextflow run dummydataset.nf --epoch 10 -c nextflow.config -resume

It fails the nextflow.config due to unknown config attribute PYTHONPATH

ruiqi@DESKTOP-BJB5T72:~/BE 223B/Naylor/DRFNS-master$ nextflow run dummydataset.nf --epoch 10 -c nextflow.config -resume
N E X T F L O W  ~  version 19.10.0
Launching `dummydataset.nf` [jolly_magritte] - revision: 176bd474ac
Unknown config attribute `PYTHONPATH` -- check config file: /home/ruiqi/BE 223B/Naylor/DRFNS-master/nextflow.config

Have you ever encountered such bug?

[PeterJackNaylor]

Hi,
I have never encountered this error before...
Are you still encountering it? I can think of a workaround but it will get ugly...

[GekFreeman]

Maybe this is a problem with nextflow version
I fixed this bug by modifying nextflow.config as follows:
env { PYTHONPATH = "$PWD/src_RealData:\$PYTHONPATH" }

[lucas-sancere]

Hi,

I had the exact same issue as @tinahuang222.

I fixed it by modifying nextflow.config not with this spelling:
env { PYTHONPATH = "$PWD/src_RealData:\$PYTHONPATH" } , leading to a new error,

but with this one:
env { PYTHONPATH = "$PWD/src_RealData:$PYTHONPATH" }

[PeterJackNaylor]

Hi,

Thanks for your input.
Are you still have any problems?