not sure, why but the bwa step does not give me a non-zero exit status...-o pipefail is set as well as set -e...minor issue, b/c when bqsr gives a non-zero and everything else fails, i can assume that everything failed starting at bwa...but still weird.
not sure, why but the bwa step does not give me a non-zero exit status...-o pipefail is set as well as set -e...minor issue, b/c when bqsr gives a non-zero and everything else fails, i can assume that everything failed starting at bwa...but still weird.