Fix missing/wrong SENTIEON_DEDUP stub output

[alkc]

fixes nf-core/raredisease#462

Description

The stub files created by SENTIEON_DEDUP do not match that of the main process.

This update fixes that by adding the missing files and modifying the stub code so that bam/bai or cram/crai files are created depending on the process input, instead of only creating a cram and crai by default.

Example

Discovered when trying to do a stub run in in the raredisease pipeline:

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP (hugelymodelbat)'

Caused by:
  Missing output file(s) `*.bai` expected by process `NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP (hugelymodelbat)` (note: input files are not included in the
efault matching set)

Command executed:

  touch hugelymodelbat_dedup.cram
  touch hugelymodelbat_dedup.cram.crai
  touch hugelymodelbat_dedup.metrics
  touch hugelymodelbat_dedup.score

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP":
      sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
  END_VERSIONS

Command exit status:
  0

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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[alkc]

There. The PR is ready for review. The first commit accidentally removed the bam/cram file from the stub output.

I've confirmed in the raredisease pipeline that the stub works as it should now.

[maxulysse]

Tests are failing for now, cause I need to restart the license server