Pass target-bed-file to bcftools/stats?

[asp8200]

Description of feature

Do we want to pass a target-bed-file to the module BCFTOOLS_STATS in subworkflows/nf-core/vcf_qc.nf? By supplying a target-bed-file to BCFTOOLS_STATS, we (supposedly) get some nice depth-plot.

With the target-bed-file but without the tbi-file for the vcf-input-file, BCFTOOLS_STATS throws the following error:

nextflow run main.nf -profile test,tools_tumoronly,singularity --tools manta

resulted in the following error:

  Process `NFCORE_SAREK:SAREK:VCF_QC:BCFTOOLS_STATS (sample2)` terminated with an error exit status (255)

Command executed:

  bcftools stats \
       \
      --regions-file multi_intervals.bed \
      sample2.manta.tumor_sv.vcf.gz > sample2.manta.tumor_sv.bcftools_stats.txt

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:VCF_QC:BCFTOOLS_STATS":
      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Command error:
  [E::idx_find_and_load] Could not retrieve index file for 'sample2.manta.tumor_sv.vcf.gz'
  Failed to read from sample2.manta.tumor_sv.vcf.gz: could not load index

Work dir:
  /home/aspe/dev/fork_sarek/work/9b/0c3268ad4e17ee489871c6849292ff

The advantage of passing the target-bed-file to bcftools-stats, would be that then we get a depth-plot for wes-samples.

@SusiJo wrote the following on Slack explaining the problem in detail: "My problem was that I do not have any real WES data to test this properly, only the testdata itself. If the depth plot is really not displayed correctly in the multiqc report for real data without a target-bed file, then i would say it’s worth the effort. An empty plot in a multiqc is really weird and confusing. There are some modules in multiqc that state explicitly when there’s nothing to plot (like a warning). It would be nice to have sth like that for bcftools as well rather than showing an empty plot.
For some testdata cases there were these empty plots, but i assumed there would be depths to plot for real data.
So before changing the module upstream and a lot of stuff in sarek with these tbiand vcf files i’d like to know if anyone who ran with real WES data has seen empty depth plots.. or if that’s really just a problem with the testdata.. If it’s just a testdata issue, it might even make sense to remove the target_bed from the bcftools module again. "