add CRAM input handling

[alkaZeltser]

CRAM formatted inputs require some modifications of the pipeline:

1. PipeVal requires access to the reference file used for CRAM compression.
2. CollectHsMetrics requires access to the reference fasta and index files.

[alkaZeltser]

@yashpatel6 any thoughts regarding PipeVal handling? Is there a way to provide it a reference file through the pipeline?

[yashpatel6]

I think the way forward will be to generalize the PipeVal process used within Nextflow to allow additional inputs and options

[alkaZeltser]

I think the way forward will be to generalize the PipeVal process used within Nextflow to allow additional inputs and options

Sorry I don't understand, are you recommending changes to the external PipeVal tool independent of pipeline-targeted-coverage or are you recommending changes internal to pipeline-targeted-coverage, e.g. modifying this code?

[yashpatel6]

I mean the Nextflow process we have for PipeVal (ie. the one being imported here: https://github.com/uclahs-cds/pipeline-targeted-coverage/blob/f3a5959d24538b445f83b1438786a2b9e92f13b8/main.nf#L6) needs to be generalized to allow for additional options