Hello people! I found myself in a bit of predicament while updating the PureCN module. Given a prefix of

foo

, I expect outputs like •

foo_loh.csv

•

foo_amplification_pvalues.csv

•

foo.csv

(new, what I want to add) I obviously can't use

*.csv

as a glob, and I wouldn't use

${meta.id}

because the user can choose a different prefix. Any suggestions?

In such cases, you remove "def" when defining the prefix and you use ${prefix}.csv to capture that..and you ll probably need to use ${prefix}_loh.csv to capture the other one

Well, I expect either

meta.id

or a prefix... how do I handle such a case? Or I just focus on one? The others are easier because I can do

*_loh.csv

, it's just this one that is a plain

.csv

.

prefix is your friend, because it is either equal to meta.id

prefix = task.ext.prefix ?: "${meta.id}"

or you overwrite it through the modules configuration file. so the outputs should be:

output:
    tuple val(meta), path("${prefix}_loh.csv")                  , emit: loh
    tuple val(meta), path("${prefix}_amplification_pvalues.csv"), emit: amp
    tuple val(meta), path("${prefix}.csv")                      , emit: csv
    path "versions.yml"                                         , emit: versions

something like this

Oh, I get it.

def

makes the variable local, doesn't it?

Yep!

OK, this should be enough to get the ball running (and make the stub tests pass, at least...)