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I was trying to debug an error in the RScript generated after base recalibration, while running the DataProcessingPipeline.scala (run as it is).
I get the following debug output
[...] Error in file(filename, "r", blocking = TRUE) : cannot open the connection Calls: source ... eval.with.vis -> eval.with.vis -> gsa.read.gatkreport -> file In addition: Warning messages: 1: In file(filename, "r", blocking = TRUE) : cannot open file '/SAN/scratch3/sample378_TTAGGC_L004_R1_001.fastq.pre_recal.table.recal': No such file or directory Execution halted
no file ending with "recal.table.recal" exists, but the file "recal.table" does exist.
I couldn't find any step in the scala script where a ".recal" is added to "recal.table", nor a specific trait or class referring to the RScript itself, as I understand it's part of the walker BaseRecalibrator.
is this a small bug in the name handling, or am I doing something wrong somewhere?