Switches bwa mem from 0.7.5a to 0.7.12 using the same parameters as before in the CWL, except this removes the pipe into samtools view and instead outputs a SAM file, due to memory issues.
Adds a separate samtools view CWL step to convert the outputted SAM to a BAM.
Switches
bwa memfrom 0.7.5a to 0.7.12 using the same parameters as before in the CWL, except this removes the pipe intosamtools viewand instead outputs a SAM file, due to memory issues.Adds a separate
samtools viewCWL step to convert the outputted SAM to a BAM.