✏️ added sort chr blocks to concatenateVCFs.sh

[bhagesh-h]

Modifications to concatenateVCFs.sh

• Made chromosome blocks continuous using bcftools sort function and removed temporary files generated to prevent bcftools error ( To prevent Command error:[E::hts_idx_push] Chromosome blocks not continuous tbx_index_build failed: rawcalls.vcf.gz).
• Complete error log :

Error executing process > 'ConcatVCF (HaplotypeCallerGVCF-1234N)'

Caused by:
  Process `ConcatVCF (HaplotypeCallerGVCF-1234N)` terminated with an error exit status (1)

Command executed:

  concatenateVCFs.sh -i GRCh38_no_alt_analysis_set.fasta.fai -c 8 -o HaplotypeCaller_1234N.g.vcf -t CEV4_no_alt.bed

Command exit status:
  1

Command output:
  (empty)

Command error:
  [E::hts_idx_push] Chromosome blocks not continuous
  tbx_index_build failed: rawcalls.vcf.gz

Work dir:
  /home/local/Documents/nextpipe/test/work/ce/25595d5ebe2a6c6e9037ec8b5e0d32

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @bhagesh-codebeast,

It looks like this pull-request is has been made against the bhagesh-codebeast/sarek master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the bhagesh-codebeast/sarek dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[FriederikeHanssen]

Have merge #432 which offers a similar solution