Penn SCAP-T Pipeline: Documentation
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Module: RSYNC
This module will copy all processed files and log file to the analyzed directory in the data repository. The data will be placed in a subdirectory in the analyzed directory with the sample ID being the name of the subdirectory.
Usage:
ngs.sh rsync [-o outputDir] sampleID
Output
all subdirectories in sampleID except 'orig' are copied to analyzed\sampleID
Options:
-o - directory containing subdirectory with analysis files (default: ./analyzed). This is the parent directory of the sample-specific directory. The sampleID will be used to complete the directory path (ie outputDir/sampleID).
Copies all data to 'outputDir/sampleID' directory. This will not copy the files in the sampleID/orig directory. Rsync is run twice as a consistency check.