These are chat archives for nextflow-io/nextflow

17th
Feb 2016
Endre Sebestyén
@razZ0r
Feb 17 2016 15:22
Hi, I just wrote my first pipeline, but I'm definitely not getting something. Here is the script: https://gist.github.com/razZ0r/b28328788b814d88fe54 Problem is, quantify_kallisto is executed only once, but I have two tar.gz archives (sample1.tar.gz, sample2.tar.gz) in the test directory. What is the problem? Thanks!
Endre Sebestyén
@razZ0r
Feb 17 2016 15:32
working, thanks!
Evan Floden
@evanfloden
Feb 17 2016 15:34
No worries! If you want to check out my Kallisto implementation see: https://github.com/cbcrg/kallisto-nf
It still needs a bit to sort out but you get the basic idea.
Paolo Di Tommaso
@pditommaso
Feb 17 2016 15:39
Hi, you could also uncompress the read file in the quantify_kallisto process
just before running kallisto.
At the there's no advantage to have a separate process only to extract the read files
Endre Sebestyén
@razZ0r
Feb 17 2016 15:49
I'm planning to run multiple tools (and maybe different transcript annotations) on the fastq files, so that's why I extracted them in a separate process. Kallisto is just one tool I started with.
Paolo Di Tommaso
@pditommaso
Feb 17 2016 15:49
:+1: