Preserve realigned bam file when using gatk for genotyping

[aidaanva]

For both visual inspection of bam files and upstream analysis, it will be great if the realigned bam file can be kept when running the gatk genotyping.

[jfy133]

To stop cluttering up output, I will make this optional with a flag, so a user can explicitly call it.

[jfy133]

Same context - add check that a JAR is actually supplied (ending in jar)

[aidaanva]

Thank you for adding the flag. I have an extra request, would it be possible that when the flag is specified the bam file gets also indexed? We usually use the realigned bam files for visual inspection in IGV and that would be useful.

[apeltzer]

Hi @aidaanva ! Yes, sure. Should be easy to have something like this:

def run_indexing = params.saveIntermediates ? 'samtoolx index bamfile' : ''
script
"""
...
$run_indexing
"""

(and have an optional output statement in the output: section of that particular step 👍

[apeltzer]

Should be fixed in #495