(Nextflow) Having trouble with a generic process to stitch together files that were split and then processed

Question

[sodiumnitrate]

I'm new to nextflow and I'm trying to figure out how to:

1. Get a large .fasta file, split it into pieces of size 1000
2. Apply same python script to each piece.
3. Pass the list of files to a process to cat them into one file.

I have something like this:

params.infile = "huge.fasta"
params.size = 1000

process filter_seq {
    input:
    file x

    output:
    path "filtered_${x}.fasta"

    script:
    """
    python $projectDir/filter.py $x filtered_${x}.fasta
    """
}

process collect_split_proc {
    publishDir 'results', model: 'copy'

    input:
    var out_name
    path x

    output:
    path out_name

    script:
    """
    < $x cat >> $out_name
    """
}


workflow {
    Channel.fromPath(params.infile) | splitFasta(by: params.size, file: true) | filter_seq

    collect_split_proc("filtered.fasta", filter_seq.out) | collectFile

}

However, this results in the error:

Process `collect_split_proc` declares 1 input channel but 2 were specified

I want to be able to pass out_name to the collect_split_proc process because I will be doing other operations down the line that also require the file to be split and then stitched back together, so I want to re-use it. I'm also a newbie, so I suspect that there's a trivial way to cat results of splitFasta | process into a specific file. Is there such a thing? If not, what is wrong with my process?

Note: the python script has two command line arguments: input_file_name, output_file_name.

Answer 1

[Pierre Lindenbaum]

`var out_name` -> `val(out_name)`