These are chat archives for nextflow-io/nextflow

21st
Nov 2018
Phil Ewels
@ewels
Nov 21 2018 10:43
That's what we'd like - take battle tested production pipelines and make it easier for people to run them without much knowledge of nextflow
I teach a few courses where I introduce our pipelines and most of the students are pretty familiar with the shared computing cluster (disk quotas, project identifiers etc), but running a nextflow pipeline takes another level of experience
eg. single hyphens versus double, resuming, which parameters are required and which are not and so on
There I think a GUI (or an interactive command line UI) would be really helpful to guide them through the process, instead of saying "go and read this 20 page long documentation before you try anything"
Paolo Di Tommaso
@pditommaso
Nov 21 2018 10:46
let's talk about that, the QBiC is not working on that ?
Alexander Peltzer
@apeltzer
Nov 21 2018 10:50
I think we were collecting ideas and thoughts on what would be needed
Once this is there I’d be happy to start working on something like this
Paolo Di Tommaso
@pditommaso
Nov 21 2018 10:51
ok, tomorrow it's a good opportunity to discuss on this
Alexander Peltzer
@apeltzer
Nov 21 2018 10:52
There was already discussions whether to do it in python / groovy ... and how we could have Such a GUI dynamically be created on the basis of a script for example :)
Yes absolutely :+1:
Paolo Di Tommaso
@pditommaso
Nov 21 2018 10:53
there's also this project that seems interesting https://github.com/UMMS-Biocore/dolphinnext
Paolo Di Tommaso
@pditommaso
Nov 21 2018 11:32
maybe it's not immediately clear, but it's a front-end for nextflow pipelines https://dolphinnext.readthedocs.io/en/latest/dolphinNext/process.html
Daniel E Cook
@danielecook
Nov 21 2018 11:45
Is there a way to split a set across multiple lines? Or perhaps there is an approach to avoiding very long set lines in input/output parameters...
e.g.
set val(species), val(length), val(max_mismatch), file("${species}_${length}_${max_mismatch}.mappability"), file("index.gem") into mappability

into...

set val(species),
    val(length),
    val(max_mismatch),
    ...etc.
Alexander Peltzer
@apeltzer
Nov 21 2018 11:52
maybe it's not immediately clear, but it's a front-end for nextflow pipelines https://dolphinnext.readthedocs.io/en/latest/dolphinNext/process.html
Nice!
Need to have a look pretty soon but catching a bus now for the airport - see you later!
Daniel E Cook
@danielecook
Nov 21 2018 12:28
@evanfloden Thanks that is very helpful!