Fix bcftools mpileup

[amnghn]

Description of feature

Some versions of samtools and bcftools are not compatible so the pileup file generated by samtools mpileup cannot be read by bcftools call. Also, it seems bcftools call accepts only a piped input from bcftools mpileup. So the pileup files generated by samtools mpileup cannot finally be used for variant calling! I know there might be some ways to figure it out without adding a new feature to the pipeline but I have two suggestions to make Sarek even better:

1. Replace samtools mpileup with bcftools mpileup.
2. Add bcftool call for actual variant calling and generate the final vcf file.

[FriederikeHanssen]

Hey as discussed bcftools is already included. actually so is call and the final vcf files should be outputted: https://github.com/nf-core/sarek/blob/6c0d335e17fb4406f527540631da7b26a5fe1464/modules/nf-core/bcftools/mpileup/main.nf#LL36C5-L36C5