relipmoc / skewer

MIT License
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Set custom path for output #43

Closed royfrancis closed 6 years ago

royfrancis commented 6 years ago

Is it possible to set a different path for the output files other than the current working directory?

skewer \
-x "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" \
-y "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA" \
-m pe \
-u \
-n \
-k 6 \
-l 20 \
-o sampleA \
sampleA_1.fq.gz sampleA_2.fq.gz

Since the documentation says -o is a base name, -o, --output <str> Base name of output file; ('<reads>.trimmed')

I was wondering if adding a path prefix would work? -o /home/custompath/sampleA

ATpoint commented 6 years ago

Of course. Standard rules of the command line apply, -o /path/to/directory/sampleA