Maybe the Nextflow problem

[sam-mic]

Hi,

I tried to install the nextflow with conda and git clone the project

I run an example with the recommend command and encountered an error. I'm not familiar with nextflow and could anyone help me with it? Thanks. The following is the error message:

N E X T F L O W ~ version 19.01.0 Launching ../main.nf [festering_lumiere] - revision: 90e74631b4 ERROR ~ The current scope already contains a variable of the name it @ line 215, column 47. alleles.out.new_pbp.subscribe { it -> ^

_nf_script_49bbb228: 238: The current scope already contains a variable of the name it @ line 238, column 47. alleles.out.new_pbp.subscribe { it -> ^

_nf_script_49bbb228: 261: The current scope already contains a variable of the name it @ line 261, column 47. alleles.out.new_pbp.subscribe { it -> ^

_nf_script_49bbb228: 322: The current scope already contains a variable of the name it @ line 322, column 44. LST.out.new_alleles.subscribe { it -> ^

_nf_script_49bbb228: 325: The current scope already contains a variable of the name it @ line 325, column 39. MLST.out.pileup.subscribe { it -> ^

5 errors

[blue-moon22]

Hi there,

Apologies for the delayed response. Which directory are you running this in? It seems like you're launching it within another directory. Try running it again in the GPS-Typer-sanger-nf directory itself (but using the path main.nf etc..)