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wodanaz / Assembling_viruses

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Improve check that user has run setup script #30

Closed johnbradley closed 3 years ago

johnbradley commented 3 years ago

The run-escape-variants.sh script contains a check that the genome file has been setup using setup-escape-variants.sh. This check assumed that bwa idx creates a file with a ".fai" extension. This may not always be the case for bwa.

Changes here simplify this check to just look for a ".dict" file that is explicitly created by create-picard-dictionary.sh. This is the last step in setup-escape-variants.sh.

Fixes #29