BCFTOOLS ROH and multiple lanes - sample names duplicated in command

[lfearnley]

Description of the bug

I'm encountering the below issue, which I think is being caused by having a sample with two lanes in the sample sheet.

If I change into the work directory and run bcftools roh with only the one sample name, it runs without issue. If I run it with the same sample name twice as in the command, I get the same error.

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:BCFTOOLS_ROH (xiv)'

Caused by:
  Process `NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:BCFTOOLS_ROH (xiv)` terminated with an error exit status (255)

Command executed:

  bcftools \
      roh \
      --samples A344892,A344892 --skip-indels  \
      --AF-file gnomad_sites.tab.gz \
       \
       \
       \
       \
      -o xiv_roh.roh \
      xiv_split_rmdup.vcf.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RAREDISEASE:RAREDISEASE:ANNOTATE_SNVS:BCFTOOLS_ROH":
      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  WARNING: While bind mounting '/vast:/vast': destination is already in the mount point list
  The 2-th sample not found in the VCF: A344892,0

My sample sheet, replacing file paths with # for readability, looks like:

sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id
A344892,1,#,#,1,2,A368331,A366201,xiv
A344892,2,#,#,1,2,A368331,A366201,xiv
A368331,1,#,#,1,1,,,xiv
A368331,2,#,#,1,1,,,xiv
A366201,1,#,#,2,1,,,xiv

Command used and terminal output

No response

Relevant files

No response

System information

Current git repo version.

[ramprasadn]

Fixed #420