liftover_variants.sh not removing index file

[svandenhoek]

How to reproduce:

sbatch --output=/path/to/train_test_liftover_grch38.log --error=/path/to/train_test_liftover_grch38.err ./liftover_variants.sh -i /path/to/train_test.vcf.gz -o /path/to/train_test_grch38

Stdout:

CLA passed
Loading Picard
Running Picard
Gzipping outputs
Removing indexing file if made
Done

Seems Indexing file removed echo is missing, so if statement is not triggered.

Expected output files:

• train_test_grch38.vcf.gz
• train_test_grch38.vcf_rejected.vcf.gz

Actual output files:

• train_test_grch38.vcf.gz
• train_test_grch38.vcf.idx
• train_test_grch38.vcf_rejected.vcf.gz