These are chat archives for nextflow-io/nextflow

15th
Feb 2017
LukeGoodsell
@LukeGoodsell
Feb 15 2017 10:20
Hi @pditommaso, thanks for implementing the JSON/YAML parameters file parsing. How do I get the file to be parsed?
$ ./cat.nf --params-file parameters.yaml
N E X T F L O W  ~  version 0.23.4-SNAPSHOT
Launching `./cat.nf` [mad_mclean] - revision: 8d1c556771
[params-file:parameters.yaml, paramsFile:parameters.yaml]
Paolo Di Tommaso
@pditommaso
Feb 15 2017 10:21
Hi, it's -params-file not --params-file ;)
LukeGoodsell
@LukeGoodsell
Feb 15 2017 10:21
Doh! Thanks. Working nicely now.
Paolo Di Tommaso
@pditommaso
Feb 15 2017 10:22
:+1:
amacbride
@amacbride
Feb 15 2017 19:50
I'm looking forward to trying the parameter file support -- I had implemented my own using
def configfile = new File(params.configLocation.toString())
def config = new JsonSlurper().parseText(configfile.text)
params.config = config
...but I'll always prefer to use built-in support if I can! :)
@pditommaso I'm getting the following warning with 0.23.2, and I'm not sure why:
WARN: [recalAnalyze (E06_RD00339B)] StoreDir can only be used when using 'file' outputs
But the output for that process is defined as:
  output:
                val file("recalplots.csv") into recal_covariates
Is there something I'm missing?
Paolo Di Tommaso
@pditommaso
Feb 15 2017 20:02
You should not use val there, it should be
output:
                file("recalplots.csv") into recal_covariates
amacbride
@amacbride
Feb 15 2017 20:03
perfect, thanks!