Running with same sample and case name crashes in RENAME_FILES

[Jakob37]

Description of the bug

I am running a single sample, and ended up assigning the same ID for both "sample" and "case" columns in the input samplesheet.

This crashes in a step where Tomte attempts to softlink the same name to itself.

Not 100% the identical case/sample is the reason, but would suspect so. Will try changing the case and rerun.

I am working on a branch from #147, so if later fixed in dev, this is a non-issue.

Command used and terminal output

ERROR ~ Error executing process > 'GENOMICMEDICINESWEDEN_TOMTE:TOMTE:ALLELE_SPECIFIC_CALLING:RENAME_FILES (<ID>)'

Caused by:
  Process `GENOMICMEDICINESWEDEN_TOMTE:TOMTE:ALLELE_SPECIFIC_CALLING:RENAME_FILES (<ID>)` terminated with an error exit status (1)


Command executed:

  ln -s <ID>.vcf.gz <ID>.vcf.gz

  cat <<-END_VERSIONS > versions.yml
  "GENOMICMEDICINESWEDEN_TOMTE:TOMTE:ALLELE_SPECIFIC_CALLING:RENAME_FILES":
      ln: $(echo $(ln --version 2>&1 | head -n 1 | cut -d ' ' -f4))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  ln: <ID>.vcf.gz: File exists

Work dir:
  /<work>/10/05e1e81edf6d6dc5f5f06df112c207

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- 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

### Relevant files

_No response_

### System information

_No response_

[Lucpen]

Hi Jakob,
I don't think it should be allowed to have the same sample and case ID as tracking output files is more simple, if you would add another sample you could end up with a case called as one of the sample with another sample in side or you could end up with a trio named after the patient.

Perhaps we could add a check at the very start of the pipeline? That way it would complain right away and it just won't run. Does that sound reasonable?

[Jakob37]

Yes, that makes sense!