Is this the good way to handle one or many inputs?

input:
    tuple val(meta), path(reads)
    ....

    """
    fastcat \\
        $args \\
        --threads $task.cpus \\
        --sample ${prefix} \\
        ${reads.join(' ')} 2&>1 /dev/null <--- this
    """

I think that by default

${reads}

will expand to

file1.ext file2.ext file3.ext ...

If you need to give them each a flag (e.g.

-i

) you can do something like: https://github.com/nf-core/modules/blob/96398d76ad719f9b57f27ff39c09834b7815461b/modules/nf-core/sentieon/dedup/main.nf#L36

Thanks a ton, I'll test that out.

I did wonder what the redirect was for

Correct me if I'm wrong, but I think a single input file will not be a list and the

join

method will not be found in this case. Therefore, you should use

path(reads, arity: '1..*')

to always force it into a list.

What's the arity option for?

The

arity: '1..*'

will make sure that

reads

is always a list, even if only a single input file is provided. This will make sure that the

reads

object will always have a

join

method to call. But of course, you don't need the

join

at all in this case.

Oh thats a cool feature, thanks for explaining.