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
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