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input and output directories #17

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csoneson opened this issue Sep 14, 2018 · 2 comments
Closed

input and output directories #17

csoneson opened this issue Sep 14, 2018 · 2 comments
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In the config file, allow the user to specify an input directory (where the fastq.gz files are), as well as an output directory (recommended default .) where the output will be generated.
@fionarhuang fionarhuang self-assigned this Sep 25, 2018
@csoneson
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csoneson commented Oct 6, 2018

Largely addressed in 6f8c346. However, snakemake is not happy with relative paths starting with ./

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csoneson commented Oct 9, 2018

The relative paths issue is addressed in 7a1bb63

@csoneson csoneson closed this as completed Oct 9, 2018
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@csoneson @fionarhuang