Running in `-stub` mode fails for BISMARK_SUMMARY

[bounlu]

Description of the bug

This line seems to cause the issue. Because bam is specified as a value channel rather than path.

-[nf-core/methylseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_METHYLSEQ:METHYLSEQ:FASTQ_ALIGN_DEDUP_BISMARK:BISMARK_SUMMARY'

Caused by:
  No signature of method: nextflow.util.ArrayBag.baseName() is applicable for argument types: () values: []
  Possible solutions: average(), average(groovy.lang.Closure), hashCode(), hashCode(), stream(), stream() -- Check script '/home/.nextflow/assets/nf-core/methylseq/workflows/methylseq/../../subworkflows/nf-core/fastq_align_dedup_bismark/../../../modules/nf-core/bismark/summary/main.nf' at line: 36


Source block:
  def args = task.ext.args ?: ''
  def prefix = task.ext.prefix ?: "${bam.baseName()}"
  """
  touch ${prefix}.report.txt
  touch ${prefix}.report.html
  
  cat <<-END_VERSIONS > versions.yml
  "${task.process}":
      bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')
  END_VERSIONS
  """

Container:
  quay.io/biocontainers/bismark:0.24.2--hdfd78af_0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

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

Command used and terminal output

nextflow run nf-core/methylseq \
-stub \
-profile docker \
...

Relevant files

No response

System information

No response

[sateeshperi]

@bounlu should be fixed. plz try again and close issue if works as expected