nf-core / bamtofastq

Converts bam or cram files to fastq format and does quality control.
https://nf-co.re/bamtofastq
MIT License
16 stars 13 forks source link

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

Open SumeetTiwari07 opened 5 months ago

SumeetTiwari07 commented 5 months ago

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 commented 5 months ago

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

SumeetTiwari07 commented 5 months ago

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