These are chat archives for nextflow-io/nextflow

25th
Nov 2016
Tiffany Delhomme
@tdelhomme
Nov 25 2016 13:26
hi @pditommaso , is this expected?:
nextflow run helloworld -C config.txt
      Unknown option: -C -- Check the available commands and options and syntax with 'help'

nextflow -version

      N E X T F L O W
      Version 0.22.5 build 4102
      last modified 17-11-2016 10:46 UTC (11:46 CEST)
      http://nextflow.io
Maxime Garcia
@MaxUlysse
Nov 25 2016 13:27
its -c not -C I guess
Tiffany Delhomme
@tdelhomme
Nov 25 2016 13:29
nextflow help
Usage: nextflow [options] COMMAND [arg...]

Options:
  -C
     Use the specified configuration file(s) overriding any defaults
  -D
     Set JVM properties
  -bg
     Execute nextflow in background
  -c, -config
     Add the specified file to configuration set
I would like to use only the specified config file
Paolo Di Tommaso
@pditommaso
Nov 25 2016 13:50
yes
it's supposed to be
nextflow  -C  run helloworld config.txt
before run
Tiffany Delhomme
@tdelhomme
Nov 25 2016 14:09
nextflow -C run helloworld config.txt 
Expected a command, got helloworld -- Check the available commands and options and syntax with 'help'
Paolo Di Tommaso
@pditommaso
Nov 25 2016 14:09
sorry my fault
nextflow  -C config.txt  run helloworld
both -c and -C are top level options, though -c is available also on the run command
Tiffany Delhomme
@tdelhomme
Nov 25 2016 14:11
hum ok! :+1: thanks