splitter/process_fastq have incomplete checks for required reference files

nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.

GNU Lesser General Public License v3.0

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Closed janders3-nmdp closed 9 years ago

janders3-nmdp commented 9 years ago

Currently, only the main chromosome_reference.fa file is checked -- but several others are required.

If we wanted to be truly fancy, the script could offer to index that reference file, in order to generate any missing reference files.

ghost commented 9 years ago

REFDIR and REFCHR are all that are used currently.