splitFasta by: variable

[JAMKuttan]

Hi I am using the nextflow scripting language and want to use the splitFasta function but split by a variable that forces a total of 50 files.

nFasta = (infasta.countFasta()/50).toInteger() + 1
infasta.splitFasta( by: $nFasta, file: true )

I am not sure how to access this value and pass it into the by statement.

[bentsherman]

Hi @JAMKuttan , since countFasta() returns a channel, you can't use it like a regular variable. You'll have to count the number of FASTA records with a custom function. You can follow this example to count the lines of a file.

[jpfeuffer]

Hi! I am trying to do the same, but I am not sure how the linked example helps.
Whenever I do:

count = 0
myFile.eachLine { str ->
    count++
}

count will not be updated outside. See also #1702 and #3388

The workaround in the issue is also not really satisfying since it involves spawning a whole process just to compute something very basic like the size of a channel.

[jpfeuffer]

Thanks for your input! Could you give me an example? Or what do you mean by "function" exactly? A process?

[bentsherman]

def myCountLines(file) {
    def count = 0
    file.eachLine{
        count++
    }
    return count
}

[jpfeuffer]

Ah I see, but in my case my file is indeed produced by a previous process and therefore comes out of a channel. Would your solution still work?

[bentsherman]

Right, so instead of MYEACHLINE(f) you would do f.map { myCountLines(it) } to get the lines in each file.

Although I should mention, since the original issue was about using splitFasta with a count based on the lines in the file, that you won't be able to do that if the file itself is coming from a channel. Because then the count is computed in a channel and you can't pull it out to pass it to the by option.

[bentsherman]

In fact, if you are doing f.map { myCountLines(it) } then you might as well do f.countLines() instead.