I want to count the number of input and output files to check all files are properly processed. -> Solved!!

count_number_of_files_in_channel.nf

#!/usr/bin/env nextflow

Channel.fromPath("*.txt")
.map{[
    file(it),
    file(it).baseName
    ]}.into{
        input_files
        input_files_
        input_files__
    }

// Get the number of files (Strictly speaking, the number of [file (it), file(it).baseName])
n_files = input_files_.count().getVal()

// Get the number of files with > 0 bytes
n_file_pos = input_files__.count {it[0].size() > 0}.getVal()
println "# of files with >0 bytes: $n_file_pos"

process line_count {
    tag { "${sample_id}"}
    publishDir "line_count/${sample_id}"

    input:
    set file(infile), sample_id from input_files

    output:
    set file("${sample_id}.out.txt"), sample_id into output_files

    script:
    def ofile = "${sample_id}.out.txt"
    """
    wc -l $infile > $ofile
    """
}

cf: https://www.nextflow.io/docs/latest/script.html#check-file-attributes

cf: https://gitter.im/nextflow-io/nextflow?at=5d07a67ae527d95added2e24