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snappy pull-processed-data: accept list of file type as argument #140

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eudesbarbosa opened this issue Nov 10, 2022 · 0 comments
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Issue
The current implementation of snappy pull-processed-data takes only one file type as argument per execution (arg: --file-type). That is slightly inconvenient for when one wants to download several file types. For example, for CADS execution both VCFs and BAM are required, so the command is called twice:

cubi-tk snappy pull-processed-data --file-type vcf ...
cubi-tk snappy pull-processed-data --file-type bam ...

Possible Solution
Change argument --file-type from string to list. Change the impacted methods accordingly.

cubi-tk snappy pull-processed-data --file-type bam,vcf ...

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