Re: GWL pipelined process composition ?

[zimoun <zimon.toutoune@gmail.com>]

Hi Roel,

Thank you for all your comments.


> Maybe we can come up with a convenient way to combine two processes
> using a shell pipe.  But this needs more thought!

Yes, from my point of view, the classic shell pipe `|` has two strong
limitations for workflows:
 1. it does not compose at the 'process' level but at the procedure 'level'
 2. it cannot deal with two inputs.

As an illustration for the point 1., it appears to me more "functional
spirit" to write one process/task/unit corresponding to "samtools
view" and another one about compressing "gzip -c". Then, if you have a
process that filters some fastq, you can easily reuse the compress
process, and composes it. For more complicated workflows, such as
RNAseq or other, the composition seems an advantage.

As an illustration for the point 2., I do not do with shell pipe:

  dd if=/dev/urandom of=file1 bs=1024 count=1k
  dd if=/dev/urandom of=file2 bs=1024 count=2k
  tar -cvf file.tar file1 file2

or whatever process instead of `dd` which is perhaps not the right example here.
To be clear,
  process that outputs fileA
  process that outputs fileB
  process that inputs fileA *and* fileB
without write on disk fileA and fileB.



> If you have an idea to improve on this, please do share. :-)

I do not know where to look. :-)
Any ideas ?


All the best,
simon