add bcftools sort step before tabix index

[priesgo]

Add bcftools sort step before tabix index to deal with different Unix sort versions in the Concatenate_VCFs.sh script.

The motivation for this PR was making Sarek work in my system using a conda environment, not docker. My system is GNU core utils version 8.22. Tabix was complaining about the order of chromosomes after concatenation, sorting the VCF before calling tabix fixes the issue.

This is the particular command I used:

nextflow run tron-bioinformatics/sarek -r $SAREK_VERSION --input $input --outdir $output \
--step variant_calling --tools HaplotypeCaller \
--genome custom \
--fasta $REFERENCE_GENOME_FASTA --fasta_fai $REFERENCE_GENOME_FASTA_INDEX \
--dict $REFERENCE_GENOME_DICT \
--intervals $BED \
--dbsnp $DBSNP --dbsnp_tbi $DBSNP_TABIX \
--germline_resource $GNOMAD \
--igenomes_ignore \
 -profile conda,standard,finish

[bhagesh-h]

Hi @priesgo I have submitted a pull request for the same issue, details can be found here:
#442 (comment)

Hope it gets integrated.

[priesgo]

Indeed same issue, similar solution. Whoever reviews, please, merge one, close the other.

[FriederikeHanssen]

LGTM, sorry it toook so long. I am integrating the changes now. @bhagesh-codebeast chose to integrate this PR, because i can merge it without solving any conflicts. The solution is similar :) Thanks a lot for contributing this

[priesgo]

Welcome @FriederikeHanssen, happy that it went in.