MultiQC error with test profile using kubernetes about missing multiqc_plots

[SumeetTiwari07]

Description of the bug

Hi,
I tested the pipeline using a cluster configured to use Kubernetes.
The multiqc is unable to find the multiqc_config.yml

Command used and terminal output

$ nextflow run ./bamtofastq/ -profile test --outdir './results'

Error:
ERROR ~ Error executing process > 'NFCORE_BAMTOFASTQ:BAMTOFASTQ:MULTIQC'

Caused by:
  Process `NFCORE_BAMTOFASTQ:BAMTOFASTQ:MULTIQC` terminated with an error exit status (2)

Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
      .
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_BAMTOFASTQ:BAMTOFASTQ:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  2

Command output:
                                                                                  
   Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]                                  
                                                                                  
   This is MultiQC v1.15                                                          
   For more help, run 'multiqc --help' or visit http://multiqc.info               
  ╭─ Error ──────────────────────────────────────────────────────────────────────╮
  │ Invalid value for '-c' / '--config': Path 'multiqc_config.yml' does not      │
  │ exist.                                                                       │
  ╰──────────────────────────────────────────────────────────────────────────────╯
                                                                                  

Command wrapper:
                                                                                  
   Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]                                  
                                                                                  
   This is MultiQC v1.15                                                          
   For more help, run 'multiqc --help' or visit http://multiqc.info               
  ╭─ Error ──────────────────────────────────────────────────────────────────────╮
  │ Invalid value for '-c' / '--config': Path 'multiqc_config.yml' does not      │
  │ exist.                                                                       │
  ╰──────────────────────────────────────────────────────────────────────────────╯
                                                                                  

Work dir:
  /shared/team/nxf_work/sumeettiwari.nf-core-hack/work/4d/109010162f09da44a88cbb57fe3ea6

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details

Relevant files

No response

System information

No response

[FriederikeHanssen]

Which version are you running? Did you manage to run any other pipeline on your cluster?

[SumeetTiwari07]

Here is the version: nf-core/bamtofastq v2.1.0
Yes, the same pipeline by changing executor to 'local'.

[famosab]

Hey @SumeetTiwari07 can you confirm whether this issue persist with v.2.1.1? :)

[Leonervin]

Did you get a solution? Currently having the same problem. Tried swapping from conda to Docker and it seems like it doesn't work either

[Leonervin]

-[nf-core/bamtofastq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_BAMTOFASTQ:BAMTOFASTQ:MULTIQC'

Caused by:
  Process `NFCORE_BAMTOFASTQ:BAMTOFASTQ:MULTIQC` terminated with an error exit status (125)


Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
       \
      .

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_BAMTOFASTQ:BAMTOFASTQ:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0' locally
  docker: error getting credentials - err: exit status 1, out: ``

  Run 'docker run --help' for more information

Work dir:
  /mnt/c/Users/USER/Desktop/work/ed/07c58223f868be3e3ba777b8ee9f58

Container:
  quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details``

[famosab]

@Leonervin What is your pipeline version and the nextflow version? Can you also provide your nextflow run command and ideally also the .nextflow.log file please?

[Leonervin]

Hi @famosab Nextflow v.25.04.2, pipeline version v2.1.1
command nextflow run nf-core/bamtofastq -profile test,docker --outdir ./results

nextflow.log

[famosab]

Can you try the current dev branch with -r dev?

nextflow run nf-core/bamtofastq -profile test,docker --outdir ./results -r dev

[Leonervin]

Can you try the current dev branch with -r dev?

nextflow run nf-core/bamtofastq -profile test,docker --outdir ./results -r dev

Are the memory requirements increased for this? Getting an error asking for dedication of 15GB RAM

[famosab]

Interesting, they should not be. But can you tell me which process is asking for more RAM? Because we can probably set the RAM lower for that process.

[famosab]

Or we can set a custom config for you to adjust to whatever memory you have available.