These are chat archives for nextflow-io/nextflow

20th
Feb 2017
LukeGoodsell
@LukeGoodsell
Feb 20 2017 08:07
Hi @pditommaso. Thank you for your help on Friday. I’ve figured out that the val taking the

input is an ArrayList of collection of files, so I have to flatten the list like this:

options.allFiles = allFiles.collectNested { it.toString() }.flatten()

to get the required structure

Just thought you may be interested.
Paolo Di Tommaso
@pditommaso
Feb 20 2017 09:36
:+1:
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:07
@pditommaso Thanks for the featured pipeline of the day ;-)
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:07
welcome
I've just sent a pull request
though I'm not still able to run it
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:08
OK, I haven't tried since this last merge
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:08
the main script is main.nf right ?
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:09
yes
Try just by removing the RunManta process
We're having problems with this one
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:09
this one what ?
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:09
this Variant Caller
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:09
ah
when I try to run it, it report an error that can't find these params
actually I don't see any of them declared at the beginning of the pipeline
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:12
I need to put that in the README file
They're declared in the config file
we're mainly using UPPMAX clusters and are using their references assemblies
But it should definitively be a good idea to explain all that somewhere
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:13
yes, but the config file allows you to override those value
I don't see how it can work in this way
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:15
You think it's not supposed to work that way ?
All these files are defined as params in the config/milou.config
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:16
unless you are using an old version of NF, any params must be declared on top of your script with a default value to make it accessing in your pipeline
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:16
Using a recent version
But defining them on the config file works
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:18
I got this (after fixing that escape)
$ nextflow run main.nf --test -profile docker
N E X T F L O W  ~  version 0.23.3
Launching `main.nf` [sick_albattani] - revision: 650c0d7c3a
ERROR ~ No such variable: params.acLoci
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:19
Ok
I understand the problem
So as long as the params are defined (either in the main.nf or in a config file that is loaded) it works
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:21
yep
Maxime Garcia
@MaxUlysse
Feb 20 2017 10:21
ok, I'll try to provide all the needed reference files from somewhere, otherwise it'll be difficult to try
Paolo Di Tommaso
@pditommaso
Feb 20 2017 10:22
exactly
I would contribute some code improvements but I need to be able to run it.