Nextflow: Singleton list conversion cause quirk behaviour

[apeltzer]

Bug report

Minimal example:

    input:
    file input_files from featureCounts_to_merge.collect()

    output:
    file 'merged_gene_counts.txt'

    script:
    //if we only have 1 file, just use cat and pipe output to csvtk. Else join all files first, and then remove unwanted column names.
    def single = input_files instanceof Path ? 1 : input_files.size()
    def merge = (single == 1) ? 'cat' : 'csvtk join -t -f "Geneid,Start,Length,End,Chr,Strand,gene_name"'
    """
    $merge $input_files | csvtk cut -t -f "-Start,-Chr,-End,-Length,-Strand" | sed 's/Aligned.sortedByCoord.out.markDups.bam//g' > merged_gene_counts.txt
    """

Expected behavior and actual behavior

I expect input_files.size() to return the size of the list, e.g. having n elements.

Actually, this depends:

• if its just one element, it returns a Path object, so path.size() returns the length of the path as a String
• if its multiple elements, it returns the list size, as expected

Steps to reproduce the problem

See above testcase

Program output

Environment

• Nextflow version: 18.10.1
• Java version: 1.8
• Operating system: no-arch

[pditommaso]

What is bla in your example? do you mean input_files ?

[apeltzer]

Updated the post, yes that's what I meant :-)

[pditommaso]

OK, this is the problem we discussed right. Therefore with input_files instanceof Path ? 1 : input_files.size() you get the list size, right?

[apeltzer]

Exactly, I used this now for the RNAseq pipeline in that way :-)

[pditommaso]

OK. being so I will change the title because it's misleading. The problem is not the File.size method but the fact that a list containing a single value is implicitly converted to the element value, causing that quirk behaviour.

[apeltzer]

Yes of course :-)

[stale[bot]]

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