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MultiQC error with test profile using kubernetes about missing multiqc_plots #86

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SumeetTiwari07 opened this issue Mar 18, 2024 · 2 comments
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@SumeetTiwari07
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SumeetTiwari07 commented Mar 18, 2024

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

@SumeetTiwari07 SumeetTiwari07 added the bug Something isn't working label Mar 18, 2024
@FriederikeHanssen
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Which version are you running? Did you manage to run any other pipeline on your cluster?

@SumeetTiwari07
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Here is the version: nf-core/bamtofastq v2.1.0
Yes, the same pipeline by changing executor to 'local'.

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