Hello,
Often when sequence data is delivered to me, I receive each sample in
several input files. Generally I want to get them into a single file
ASAP, and the filterFastq step would be a convenient place to do it. Is
there any possibility to add some way to append to an output file, or
maybe automatically combine the outputs of any files with the same
destination file. For example:
filterFastq(files=c("input1.fastq", "input2.fastq"),
destinations="output.fastq", ...)
could process both input files and write their combined output to the
one specified output file. Normal recycling rules would apply for the
"destinations" argument, and input files would be grouped by destination
file and each processed sequentially into that destination file. (This
design is kind of magic, but it avoids the annoying pattern of having to
process files one-by-one in a loop with append=FALSE for the first file
and append=TRUE for the rest. (Also appending to a compressed fastq
might not work?)
-Ryan
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