Error Unknown method about nextneopi

[riederd]

Please try to use the following format to provide paired end reads on the command line, as it si explained in the Readme under "FASTQ raw reads:":

--readsTumor /work/Projects/Neoantigens_nextNEOpi/testdata/Tumor_ERR8313719_{1,2}.fastq
--readsNormal /work/Projects/Neoantigens_nextNEOpi/testdata/Normal_ERR8313721_{1,2}.fastq

alternatively, you may use a batch file to pass on the reads (which will be the only way in future versions anyway).

Hope this helps

[Magisterh1]

Thank you! I tried to run nextNEOpi.nf using the batch file and using your recommendation from above with and without quotes. However, I always end up with "Unknown method div on ConfigObject type". Do you have an other suggestion for me? THX

[riederd]

Can you send me the .nextflow.log file

[Magisterh1]

nextflow.log

[riederd]

Thanks, can you also post the /work/Projects/Neoantigens_nextNEOpi/nextNEOpi/conf/params.config file.

[riederd]

..and please check also the cluster profile settings in /work/Projects/Neoantigens_nextNEOpi/nextNEOpi/conf/profiles.config as you are specify -profile conda,cluster . You might need to adjust the cluster profile to match your environment . See also the Profiles: cluster section in the Readme

[Magisterh1]

yes, here are the params:
params.config.txt

I am working on a Ubuntu 18.04.5 LTS. Using "-profile conda" without cluster did not change the error

[riederd]

Hmmm, can you try to update nextflow to the current version?
either by:
nextflow self-update
or:
curl -s https://get.nextflow.io | bash

[Magisterh1]

ok, done, unfortunately only the wording of the error changed: Unknown method invocation div on ConfigObject type

[riederd]

There is one more thing that I spotted in your params.config:
You need to put the path for the resourcesBaseDir under quotes, e.g.
resourcesBaseDir = "/work/Projects/Neoantigens_nextNEOpi/resources"

Please check all paths that you changed in the config files.

[Magisterh1]

OK, what worked so far: 1. update nextflow, 2. add quotes to paths in params.config.
Now I have to solve some conda problems... THX for your help!!

[riederd]

Glad, I could help. BTW we recommend using singularity instead of conda. But either should work.