CHECK_KINETICS process does not report a failing exitcode if samtools is unavailable. This results in all BAMs being marked as not containing kinetics information. Typically I think this would happen if the conda environment is not set up correctly and samtools is not available.
Some combination of flags euo pipefail etc should be identified to make this return an error instead.
CHECK_KINETICS process does not report a failing exitcode if samtools is unavailable. This results in all BAMs being marked as not containing kinetics information. Typically I think this would happen if the conda environment is not set up correctly and samtools is not available.
Some combination of flags euo pipefail etc should be identified to make this return an error instead.