Bug in the nextflow.config

PeterJackNaylor / DRFNS

This repository contains the code necessary in order to reproduce the work contained in the submitted paper: "Segmentation of Nuclei in Histopathology Images by deep regression of the distance map".

MIT License

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Bug in the nextflow.config #6

Open tinahuang222 opened 4 years ago

tinahuang222 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 3 years ago

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 commented 3 years ago

Hi,

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