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mode to consume data from stdin

Open brentp opened this issue 9 years ago • 1 comments

currently gargs expects arguments to come on stdin and uses those to fill the command-template.

gargs could have a --pass-through mode that sends --nlines of stdin to each process. In order to block as little as possible, the main process will read into a temp file and then set an io.Reader of that tmpfile as the stdin to each process.

This would enable things like:

zcat $fastq | gargs -p 20 --pass-through --nlines 100000 "bwa mem $fasta /dev/stdin"

brentp avatar Sep 22 '16 18:09 brentp

This sounds similar to xin?

chocolateboy avatar Sep 02 '17 01:09 chocolateboy