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halelab / GBS-SNP-CROP

GBS SNP Calling Reference Optional Pipeline
GNU General Public License v2.0
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Added Trimmomatic as parameter in v3 #14

Closed ne1s0n closed 6 years ago

ne1s0n commented 6 years ago

In the main branch the call to Trimmomatic is hardcoded, e.g.

system ( "java -jar /usr/local/bin/trimmomatic-0.33.jar ... [other stuff]")

I've added a command line parameter to allow customization. I had to, since I'm not using Trimmomatic 0.33 (current version is 0.36) and my install location is different. The path to Trimmomatic jar goes in the $trimmomatic variable, so that the previous line becomes:

system ( "java -jar $trimmomatic ... [other stuff]")

The default value (if not specified from argument) is set to the old hardcoded one, so that compatibility with existing scripts is preserved.

arthurmelobio commented 6 years ago

Thanks a lot @ne1s0n for your efforts on GBS-SNP-CROP. This suggestions will be release soon.

Best, Arthur