These are chat archives for nextflow-io/nextflow

30th
Jun 2016
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 12:53 UTC
Hi, any idea how can I join two and more *.nf scripts into bigger pipeline?
Paolo Di Tommaso
@pditommaso
Jun 30 2016 12:54 UTC
not supported at this time
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 12:55 UTC
primary I run nextflow in the shell inside a process but wasn't good idea? How do you usually work with it?
Paolo Di Tommaso
@pditommaso
Jun 30 2016 12:56 UTC
do you mean you have a nextflow script launching other nextflow pipelines?
nothing wrong doing that, actually that's currently the only option
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 12:57 UTC
@pditommaso not supported but there must be some workaround.
Paolo Di Tommaso
@pditommaso
Jun 30 2016 12:57 UTC
in future we want to have a proper support for sub-workflows
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 12:57 UTC
@pditommaso the problem with that approach is that I cannot see logs from internal work
Paolo Di Tommaso
@pditommaso
Jun 30 2016 12:58 UTC
I know, that's a workaround.
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 13:00 UTC
@pditommaso I thought that A workflow would print output file names paths and workflow B might take it
Paolo Di Tommaso
@pditommaso
Jun 30 2016 13:01 UTC
I'm nit getting it, an example?
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 13:02 UTC
Iam thinking of it. Do channel might take stuff from STDIN? and how?
OK. I gotta Gruvy`s System.in
Phil Ewels
@ewels
Jun 30 2016 13:09 UTC
You can use $param.varname which automatically comes from --varname <xyz>
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 13:14 UTC
but <xyz> should be produced by the earlier workflow from the chain
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 13:23 UTC
Because workflows works as shell scripts I might pipe them using bash | command. But there is no 'protocol' to communicate them. It might me json for example. I do not know groovy and don't know if there is built-in json support.
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 13:34 UTC
can I use groovy packages inside workflow files?
Jacek Grzebyta
@jgrzebyta
Jun 30 2016 15:38 UTC
I have mock example here: https://dl.dropboxusercontent.com/u/16044174/MockFlow/flow-a.nf groovy cannot parse the input file
Mike Smoot
@mes5k
Jun 30 2016 23:34 UTC
@pditommaso While I don't have a small example I can share with you, I am able to reproduce nextflow-io/nextflow#134 reliably in a branch of one of my workflows. I'm leaving for the night now, but I'd be happy to spend some time tomorrow trying to find the root cause if you can provide some guidance.