/*
 * Multi-step Nextflow pipeline demo
 *
 * Steps:
 *   1. GREET  – write a greeting to a file
 *   2. SHOUT  – convert the greeting to uppercase
 *   3. REPORT – count words and produce a summary
 *
 * Run:
 *   module load nextflow/26.04.6
 *   nextflow run multi-step.nf --name "SCC User"
 */

params.name = "World"   // override with: --name "Your Name"

// ---------------------------------------------------------------------------
// Step 1: create a greeting
// ---------------------------------------------------------------------------
process GREET {

    input:
    val name

    output:
    path 'greeting.txt'

    script:
    """
    echo "Hello, ${name}! Welcome to the SCC." > greeting.txt
    """
}

// ---------------------------------------------------------------------------
// Step 2: convert greeting to uppercase
// ---------------------------------------------------------------------------
process SHOUT {

    input:
    path greeting

    output:
    path 'greeting_upper.txt'

    script:
    """
    tr '[:lower:]' '[:upper:]' < ${greeting} > greeting_upper.txt
    """
}

// ---------------------------------------------------------------------------
// Step 3: count words and produce a short report
// ---------------------------------------------------------------------------
process REPORT {

    publishDir "results/", mode: 'copy'   // copy final output to results/

    input:
    path upper_greeting

    output:
    path 'report.txt'

    script:
    """
    WORDS=\$(wc -w < ${upper_greeting})
    echo "=== Pipeline Report ===" > report.txt
    echo "Greeting (uppercase):"   >> report.txt
    cat ${upper_greeting}          >> report.txt
    echo ""                        >> report.txt
    echo "Word count: \${WORDS}"   >> report.txt
    """
}

// ---------------------------------------------------------------------------
// Workflow: wire the processes together
// ---------------------------------------------------------------------------
workflow {
    // create a channel from the parameter value
    name_ch = Channel.of(params.name)

    // chain processes: output of each becomes input of the next
    GREET(name_ch)
    SHOUT(GREET.out)
    REPORT(SHOUT.out)
}