Minor fixes needed for maf2maf/vcf2maf wrappers

mskcc / cmo

Command-line tools for data analysts at the CMO

GNU General Public License v2.0

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Closed ckandoth closed 6 years ago

ckandoth commented 7 years ago

[x] They make temporary folders in /scratch even if the user just want to run --help
[x] cmo_vcf2maf --vcf-tumor-id defaults to TUMOR instead of the value passed into --tumor-id
[x] Separate vep path/cache to make it easier to containerize to script, while keeping the cache in a network drive
[x] 'tmp_dir' is not defined error shows up after a successful run of cmo_maf2maf.

ckandoth commented 7 years ago

Better temp folder handling implemented in 9b76e22f

ckandoth commented 6 years ago

All done in fcb98df