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
