Last 3 steps don't go into user defined output directory
diffPeaks, motifSearch, peakAnnotation goes into $baseDir/output even if the output directory is user defined.
diffPeaks, motifSearch, peakAnnotation goes into $baseDir/output even if the output directory is user defined.
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changed milestone to %1.0.0
added bug label
mentioned in commit 81054b5c
closed