CRAM to BAM Step
Converts a CRAM file to a coordinate-sorted, indexed BAM using
the supplied reference. Implemented as a workflow wrapping a
single task so it can be called either as a standalone workflow
or imported as a task from other workflows.
Task: ConvertCramToBam
Pipes samtools view (CRAM→SAM) into samtools view (SAM→BAM),
then indexes the result.
Input Parameters
- File input_cram - required - the CRAM file to convert
- String sample_name - required - used to name the outpu
This is a companion discussion topic for the original entry at github.com/mgbpm/biofx-workflows/CramToBam