Possible bug or lack of documentation regarding google batch and symbolic links

[VasLem]

I have the following process:

process readFromDirectory {
    input:
        path sample_dir
        val sample_name
    output:
        tuple val(sample_name), path("output/*.*")

    script:
        """
        mkdir -p output
        export FILES=`find $sample_dir/ -print0 | perl -0ne "print if /${sample_name}.*\\.f(?:ast)?[qa](?:\\.gz)?/s"`
        ln -sf \$FILES output/
        """    
}

which is supposed to read a folder, and return the files that match to the output. This works locally but not in the google cloud, as the symbolic link ends up dangling. I feel this is a bug, or at least there is lack of documentation explaining this edge case. followLinks is by default true, therefore one would expect to get the files and not the links to the next process, particularly not dangling ones... I have tried also other ways such as this:

process readFromDirectory {
    input:
        path sample_dir
        val sample_name
    output:
        tuple val(sample_name), path(files)

    script:
        files = sample_dir.find { it.toString() =~  /${sample_name}.*\.f(?:ast)?[qa](?:\.gz)?/ }
        """
        """    
}

which fails as the files is null (!!!!)

or even by transforming the findings into actual file names (prepending the gs bucket directory and then trying to convert that to links), like here:

process readFromDirectory {
    input:
        path sample_dir
        val sample_dir2
        val sample_name

    script:
        """
        parent_dir=`dirname $sample_dir2`
        
        export FILES=`find $sample_dir/ -print0 | perl -0ne "print if /${sample_name}.*\\.f(?:ast)?[qa](?:\\.gz)?/s" | xargs -r0 -I {} echo \$parent_dir/{}`
        """

    output:
        tuple val(sample_name), env(FILES)     
}

workflow {
        rf = readFiles(sample_dir, sample_dir, samples).collect().toList()
        Channel.fromFilePairs("$sample_dir/*", size: -1) { file -> { if file in} }
        samples_and_reads = rf.map{
            it -> 
                [it[0], it[1].split(" ").each{v -> file(v)}]
            }
}

which again fails, returning that the string (which is not a string but a list inside the list) cannot be considered as path.

I am pretty desperate and I feel I have depleted all of my options. Please help.

[VasLem]

The reason why I need this, is that I have a csv file with samples and I want to transverse a directory and get the files per sample. For example:

        samples = Channel
        .fromPath(sample_csv)
        | splitCsv(header:true)
        | map { row -> 
        row.sample_name}
        samples_and_reads = readFromDirectory(sample_dir, samples)