BWA index make parameter variable

BauerLab / ngsane

Analysis Framework for Biological Data from High Throughput Experiments

Other

34 stars 22 forks source link

BWA index make parameter variable #44

Closed BauerLab closed 10 years ago

BauerLab commented 10 years ago

BWA index '-a bwtsw' does not work on the small size of the smokebox genome, hence make this an adjustable parameter in the bwa index mod

BauerLab commented 10 years ago

Also the pipeline runs bwaIndex.sh as common task (to name the logfile) but bwaIndex.sh does not accept -o OUTFOLDER which is passed on by prepareJob submission. Hence add -o even though it does not do anything in the bwaIndex itself to avoid "don't understand -o don't understand /home/bau04c/ngsane/smokebox/common/bwa"

BauerLab commented 10 years ago

indexBWA.sh and sampleConfig have been updated