A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

I think there is still a bug about dbsnp and known_indels. I specified `dbsnp` , but not `known_indels` and I am getting:
```  A USER ERROR has occurred: Argument known-sites was missing: Argument 'known-sites' is required


Command executed:

  gatk --java-options "-Xmx9830M -XX:-UsePerfData" \
      BaseRecalibrator  \
      --input in.bam \
      --output out.table \
      --reference Homo_sapiens.fa \
      --intervals Homo_sapiens.interval_list \
       \
      --tmp-dir . \
      --use-original-qualities```
I am using 1.2.1