Incorrect meta used for bcftools sort step of gatk joint_variant_calling

[peter-yufan-zeng]

Description of the bug

I am currently trying to use Sarek to perform joint gatk4 variant calling for a WES cohort. However, I am running into an error in the NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:BCFTOOLS_SORT step where the meta freebayes is used for bcftools sorting.

I think this is due to incorrect meta used for the bcftools sort step in the joint_germline subworkflow.

Command used and terminal output

$ nextflow run ~/nf-core-sarek-3.0.1/workflow -profile singularity
	--input 20220824_isgs_sarek.csv  \
	--wes --intervals ../xgen-exome-hyb-panel-v2-targets-hg38.bed \
	-resume -c $HOME/niagara.config \
	--igenomes_base {pathtogenome} \
	--tools haplotypecaller,manta,cnvkit,snpeff \
	--joint_germline --use_gatk_spark markduplicates \
	 --nucleotides_per_second 50


Error executing process > 'NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:BCFTOOLS_SORT (joint_variant_calling)'

Caused by:
  Process `NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:BCFTOOLS_SORT (joint_variant_calling)` terminated with an error exit status (255)

Command executed:

  bcftools \
      sort \
      --output joint_variant_calling.freebayes.vcf.gz \
       \
      joint_germline.vcf.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:BCFTOOLS_SORT":
      bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
  END_VERSIONS

Command exit status:
  255

Command output:
  (empty)

Relevant files

No response

System information

Nextflow version 21.10.3, hardware: HPC, executor: slurm (although this nextflow job was submitted as local since on my cluster I can only use whole nodes (i.e 40-cores)), container: singularity, sarek version:3.0.1