Sarek Concatenate VCF option doesn't concatenate output VCFs.

[cvillaman]

Description of the bug

I'm running the Sarek pipeline on exome samples using the --wes and --concatenate_vcfs using DeepVariant, HaplotypeCaller, Freebayes and Strelka, however, the final joined VCF has only Freebayes variants.
The VCFs for each caller are generated, but they aren't being concatenated.

Command used and terminal output

nextflow run nf-core/sarek -r 3.8.1 -profile docker -resume --input {samplesheet} --genome GATK.GRCh38 --igenomes_base {refdir} --tools deepvariant,haplotypecaller,freebayes,strelka --concatenate_vcfs --max_cpus 28 --outdir {outdir}

Relevant files

No response

System information

No response