Unable to parse config file: '/a/b/nextNEOpi/conf/params.config'

[rashidma]

I have installed nextNEOpi latest version from github and all its requirements. I am using Ubuntu 18.04.

1) nextflow -version N E X T F L O W version 23.04.3 build 5875 created 11-08-2023 18:37 UTC (21:37 ADT) cite doi:10.1038/nbt.3820 http://nextflow.io 2) java -version openjdk version "11.0.19" 2023-04-18 OpenJDK Runtime Environment (build 11.0.19+7-post-Ubuntu-0ubuntu118.04.1) OpenJDK 64-Bit Server VM (build 11.0.19+7-post-Ubuntu-0ubuntu118.04.1, mixed mode, sharing) 3) singularity --version 2.4.2-dist

The command I run is as below: _NXF_VER=22.10.8 nextflow run ./nextNEOpi.nf \ --batchFile /media/mamoon/30806115-9b80-48b5-a937-40a7b4922f67/Data/NRC21R-082-03/Analysis/nextNEOpi/demo/batch_fastq.csv \ -config conf/params.config \ --outputDir /media/mamoon/30806115-9b80-48b5-a937-40a7b4922f67/Data/NRC21R-082-03/Analysis/nextNEOpi/demo/testresult \ --trim_adapters true \ --trim_adapters_RNAseq true \ --useNetChop false \ -profile singularity \ -resume

It gives following error in the log file:

_Sep-11 12:37:13.244 [main] DEBUG nextflow.cli.Launcher - $> nextflow run ./nextNEOpi.nf --batchFile /media/mamoon/30806115-9b80-48b5-a937 -40a7b4922f67/Data/NRC21R-082-03/Analysis/nextNEOpi/demo/batch_fastq.csv -config conf/params.config --outputDir /media/mamoon/30806115-9b 80-48b5-a937-40a7b4922f67/Data/NRC21R-082-03/Analysis/nextNEOpi/demo/testresult --trim_adapters true --trim_adapters_RNAseq true --use_Ne tChop false -profile singularity -resume Sep-11 12:37:13.329 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 22.10.8 Sep-11 12:37:13.370 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home /mamoon/.nextflow/plugins; core-plugins: nf-amazon@1.11.5,nf-azure@0.14.3,nf-codecommit@0.1.2,nf-console@1.0.4,nf-ga4gh@1.0.5,nf-google@1 .4.6,nf-tower@1.5.7-patch0,nf-wave@0.5.5 Sep-11 12:37:13.384 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Sep-11 12:37:13.386 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Sep-11 12:37:13.390 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode Sep-11 12:37:13.405 [main] INFO org.pf4j.AbstractPluginManager - No plugins Sep-11 12:37:13.430 [main] DEBUG nextflow.config.ConfigBuilder - User config file: /media/mamoon/30806115-9b80-48b5-a937-40a7b4922f67/sof tware/nextNEOpi/conf/params.config Sep-11 12:37:13.431 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /media/mamoon/30806115-9b80-48b5-a937-40a7b4922f67/ software/nextNEOpi/conf/params.config Sep-11 12:37:13.464 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity Sep-11 12:37:14.805 [main] ERROR nextflow.cli.Launcher - Unable to parse config file: '/media/mamoon/30806115-9b80-48b5-a937-40a7b4922f67/software/nextNEOpi/conf/params.config'

No signature of method: groovy.util.ConfigObject.div() is applicable for argument types: (Integer) values: [30806115] Possible solutions: min(groovy.lang.Closure), is(java.lang.Object), drop(int), wait(), size(), any()

groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.div() is applicable for argument types: (Integer) va lues: [30806115] Possible solutions: min(groovy.lang.Closure), is(java.lang.Object), drop(int), wait(), size(), any() at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.unwrap(ScriptBytecodeAdapter.java:70)_

Please let me know possible suggestions to solve this issue. Thanks a lot

[riederd]

Did you make any changes to the config file?

[rashidma]

I think yes. I made changes in the param.config file for "resourceBaseDir".

Is it creating trouble?

Best regards Mamoon

On Mon, Sep 11, 2023 at 2:36 PM Dietmar Rieder @.***> wrote:

Did you make any changes to the config file?

— Reply to this email directly, view it on GitHub https://github.com/icbi-lab/nextNEOpi/issues/42#issuecomment-1713703012, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE6KEOFWK6WTIUI5PPHRP33XZ3ZT3ANCNFSM6AAAAAA4TBJXZM . You are receiving this because you authored the thread.Message ID: @.***>

--

Mamoon Rashid, PhD (Bioinformatics)

Associate Research Scientist

Department of Biostatistics and Bioinformatics

King Abdullah International Medical Research Center (KAIMRC) Kingdom of Saudi Arabia

[riederd]

No it should be a problem, as long it is syntactically correct.

[rashidma]

The changes to params.config are below: // resourcesBaseDir = projectDir.toRealPath() + "/resources" resourcesBaseDir = /Data/nextNEOpi

// run CNVkit CNVkit = false

Thats all. Thank you for your time.

[riederd]

You need to quote the resources path

resourcesBaseDir = "/Data/nextNEOpi"

[rashidma]

Oh that silly mistake. It is good to go now. Thank you

[riederd]

Glad I could help