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CRG-CNAG / CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow
Mozilla Public License 2.0
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The genomeDir dir name is confusing #13

Closed pditommaso closed 4 years ago

pditommaso commented 4 years ago

The genomeDir name is used twice as a variable name:

https://github.com/CRG-CNAG/CalliNGS-NF/blob/89134343e1f8adf82332ff08631780e38689daab/main.nf#L181

and as a local directory name:

https://github.com/CRG-CNAG/CalliNGS-NF/blob/89134343e1f8adf82332ff08631780e38689daab/main.nf#L193 https://github.com/CRG-CNAG/CalliNGS-NF/blob/89134343e1f8adf82332ff08631780e38689daab/main.nf#L200

Besides it works it's really confusing when reading the task command. A different name should be used.