No such variable: params.mode

[Carlos Guzman]

Some abilities seem to have broken in 2.3.

My help menus no longer work.

if (params.help && !params.mode) {
    log.info ''
    log.info 'C I P H E R ~ version 1.0.0'
    log.info '========================================================================================================='
    log.info 'Genomics Sequencing Pipeline'
    log.info ''
    log.info 'Usage:'
    log.info '    main.nf --mode <MODE> --config <CONFIG> --genome <GENOME> --library <LIBRARY> [OPTIONS]...'
    log.info ''
    log.info 'For advanced help and optional parameters specify a pipeline mode:'
    log.info '    main.nf --mode chip    --help'
    log.info '    main.nf --mode dnase    --help'
    log.info '    main.nf --mode mnase    --help'
    log.info '    main.nf --mode gro    --help'
    log.info '    main.nf --mode rna    --help'
    log.info '========================================================================================================='
    log.info ''
    exit 1
}

Now results in a error of: No such variable: params.mode

[Paolo Di Tommaso]

You have to define params.mode to a default valid at the beginning of your script.

p

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[Paolo Di Tommaso]

*value

[Carlos Guzman]

The same problem occurs with params.help ... does that have to be set to a default value as well?

This has changed in the new version, the pervious required neither to have default values.

[Paolo Di Tommaso]

Hi Carlos, 

Yes, the latest version introduced a more strict check on user parameters (apologies if I forgot to mention it) which requires to define them before its usage. 

So, in practical term, you need to list all your params at the beginning of your script and to assign them a default value (even null). 

For example: 

https://github.com/nextflow-io/rnatoy/blob/master/main.nf#L33-L36

Hope it helps. 

Cheers,

Paolo

On Sat, Dec 17, 2016 at 7:40 PM, Carlos Guzman <cguzma...@gmail.com> wrote:

The same problem occurs with params.help ... does that have to be set to a default value as well?

This has changed in the new version, the pervious required neither to have default values.