For loop in files ending with extension in nextflow and groovy

Question

I want to write a simple nextflow pipeline where I will in one job to multiples task one after another.

Here is my file for now :

// 1. Define the input directory
params.input_dir = "path1/path2/path3/Data"

// 2. Define the output directory
params.output_dir = "path1/path2/path3/Output"

// 3. Define the process using nextflow.enable.dsl=2

process RUN_KRAKEN2 {

    publishDir params.output_dir, mode: 'copy'

    // 3.2 Define the output file
    output:
    path("Kraken2_iterations.check")

    // 3.3 Define the script
    script:
    """
    echo "Making directory"
    mkdir -p ${params.output_dir}
    for (file in file("$params.input_dir").list()) { # for each file in params.input_dir
     if (file.endsWith(".m8")) { #if it ends with *.m8
         #then do this task
         task1
         #and finaly run this last task
         task2
     }

    """
}


// 4. Run the workflow
workflow {
    RUN_KRAKEN2()
}

But there are issues in this code. I'm really new to Nextflow and especially Groovy. I've attempted to comment on each line to explain what I wanted to achieve. If someone could correct the code to be written properly, it would be amazing.

Additionally, as you can see, I've defined an output file called 'Kraken2_iterations.check'. I would like to create such a file at the end of the script, after every *.m8 file has been processed. Does anyone have an idea? I've thought of using a variable 'n=0' and then incrementing 'n' by 1 with each iteration. Then, I could use an 'if' statement like 'if n < count(files ending with *.m8)', but I'm unsure how to implement this in Groovy.

Answer 1

You can use the Groovy function eachFileRecurse(...) to iterate a folder for all files of a specific file type. This answer has an example: Recursive listing of all files matching a certain filetype in Groovy

--- Updated ---

I got this project structure:

├── data
│   ├── data.m8
│   └── input
│       ├── in.m8
│       └── out.m8
├── find-files
│   └── main.nf
└── nextflow

main.nf:

#!/usr/bin/env nextflow

process RUN_KRAKEN2 {

    script:
    def out = ''
    new File('.').eachFileRecurse(groovy.io.FileType.FILES) {
        if(it.name.endsWith('.m8')) {
            println it
            out += it
        }
    }

    """
    touch done
    echo ${out} >> done
    """
}

workflow {
    RUN_KRAKEN2()
}

Which when executed:

./nextflow run find-files/

generates a file named done in the work directory (fx. work/27/e1994e62df22bb5c7cb0ec3ef1f2cd/done) containing the files found:

./data/data.m8./data/input/in.m8./data/input/out.m8