Module to Query Access BAM paths in Voyager

[buehlere]

Create module that can query access bams from voyager.

input for module:

[id:sample, type:tumor]
[id:sample, type:tumor]
[id:sample, type:tumor]

output for module:

[
[id:sample, type:tumor, patient:name1], /path/to/bam, /path/to/bai]
],
[
[id:sample, type:tumor, patient:name2], /path/to/bam, /path/to/bai]
[id:sample, type:tumor, patient:name2], /path/to/bam, /path/to/bai]
]

Command and container should be adapted from beagle_cli: https://github.com/mskcc/beagle_cli/blob/master/apps/access/__init__.py#L49-L77

• There will need to be a parameter to get an API key.