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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_VERSIONSCommand exit status: 2Command 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/109010162f09da44a88cbb57fe3ea6Tip: 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
The text was updated successfully, but these errors were encountered:
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
Relevant files
No response
System information
No response
The text was updated successfully, but these errors were encountered: