how to turn off auto overwrite function???

[jeffchen2000]

I am using atacRepsPipe2 for a total 100 samples, it takes days to processing, which is fine though. And I think you have a good pipeline design that if the pipeline crushed due to (such as) memory issue, hard disk space issue etc.. and I can re-run the pipeline without re-creating pre-generated files.

however, in my situation, some fastq files failed to generate correct SAM files which causes down stream error. When I manually fixed the SAM file and re-run the pipeline, the manually fixed the SAM file will be over-written, I tried modify the file time stamp using touch, not work either.

now my question is how can I tune off the auto overwrite function !!!

many thanks

Chen

conclusion <- #' atacRepsPipe2( #' # MODIFY: Change these paths to your own case files! #' # e.g. fastqInput1 = "your/own/data/path.fastq" #' caseFastqInput1=list(system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"), #' system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz")), #' # MODIFY: Change these paths to your own case files! #' # e.g. fastqInput1 = "your/own/data/path.fastq" #' caseFastqInput2=list(system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz"), #' system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz")), #' # MODIFY: Change these paths to your own control files! #' # e.g. fastqInput1 = "your/own/data/path.fastq" #' ctrlFastqInput1=list(system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2"), #' system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2")), #' # MODIFY: Change these paths to your own control files! #' # e.g. fastqInput1 = "your/own/data/path.fastq" #' ctrlFastqInput2=list(system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2"), #' system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2")), #' # MODIFY: Set the genome for your data #' genome = "hg19", #' motifs = getMotifInfo(motif.file = system.file("extdata", "CustomizedMotif.txt", package="esATAC")))