LCR-BCCRC / lcr-modules

Collection of standard analytical pipelines for genomic and transcriptomic data
https://lcr-modules.rtfd.io
MIT License
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vcf2maf can't handle empty deblacklisted maf #321

Closed Kdreval closed 1 month ago

Kdreval commented 1 month ago

Found edge cases where vcf2maf is stuck at these steps:

job                          count    min threads    max threads
-------------------------  -------  -------------  -------------
_vcf2maf_normalize_prefix        2              1              1
_vcf2maf_output_maf              2              1              1
_vcf2maf_reannotate              2              4              4
all                              1              1              1
total                            9              1             12

because the reannotate rule can't handle empty maf file. The command has to be edited to handle this separately

Kdreval commented 1 month ago

The fix is in PR #318