Error after upgrading to 24.02.0-edge

[lucacozzuto]

Bug report

(Please follow this template replacing the text between parentheses with the requested information)

Expected behavior and actual behavior

Pipeline works well with version 23.10.1 With the new nextflow I got:

ERROR ~ Error executing process > 'BASECALL:DORADO_BASECALL:baseCall (mod---2)'

Caused by:
  class org.codehaus.groovy.runtime.GStringImpl cannot be cast to class java.lang.String (org.codehaus.groovy.runtime.GStringImpl is in unnamed module of loader 'app'; java.lang.String is in module java.base of loader 'bootstrap')

Source block:
  """
            dorado basecaller ${params.EXTRAPARS} --emit-fastq ./ > ${idfile}.fastq
            bgzip -@ ${task.cpus} ${idfile}.fastq
      """

[bentsherman]

Is there a stack trace for this error? It will be difficult to find the source of the error without the trace

[lucacozzuto]

do you mean the .nextflow.log?

[lucacozzuto]

I added another part of the error

[pditommaso]

Luca, please include .nextflow.log file

[lucacozzuto]

nextflow.log.txt Here it goes. Thanks!

[pditommaso]

Umm, not much more. Where's the code of that process?

[lucacozzuto]

You can see the code here:

https://github.com/biocorecrg/BioNextflow/blob/master/subworkflows/basecalling/dorado.nf

Thanks!

[pditommaso]

Is there are way to replicate it locally?

[lucacozzuto]

Ok so I tried also another pipeline that is public and got the same error. The pipeline is here:

https://github.com/biocorecrg/MOP2 For checking it you can do:

git clone --depth 1 --recurse-submodules https://github.com/biocorecrg/MOP2.git
cd MOP2
bash INSTALL.sh

cd mop_preprocess 
nextflow run mop_preprocess.nf -with-docker -profile ci

thanks again! Luca

[pditommaso]

Cannot find script file: mop_preprocess.nf

[lucacozzuto]

Cd mop_preprocess

[pditommaso]

You are right, however it fails for other reason

  Unable to find image 'biocorecrg/mopprepr:0.7' locally

Are you able to isolate the error in a smaller test case?

[lucacozzuto]

I'll try to make a smaller test case. However -with-docker should download the image (or with -singularity in case you want it).

[pditommaso]

I did it

nextflow run mop_preprocess.nf -with-docker -profile ci

[lucacozzuto]

Wow. I have a CI that is working on github and is ok :) https://github.com/biocorecrg/MOP2/blob/main/.github/workflows/build.yml

Once I have a simple test case I'll send you. Thanks again

[lucacozzuto]

I think I track down where it fails... I have this code in the nextflow.config:

clusterOptions = { "-l h_vmem=${task.memory.toString().replaceAll(/[\sB]/,'')}" }

removing it fixed the problem.

[lucacozzuto]

Hi, thanks for reopening. I'm currently not using nextflow "edge" anymore since I got java errors that are not present in the normal one.

[pditommaso]

Duplicate of https://github.com/nextflow-io/nextflow/issues/4931

[pditommaso]

Sovled by 74004fbd