Well great job! If i where you i would rather use prebuilt module from nf-core Module, Docker/Conda, enhance subworkflow to modularized the pipeline and enhance reusability. I would also have a look at nf-core best practice.

while your workflow might work this is not the usual good practice to build a NF workflow.

You should have a 'meta' associative array next to your path, the argument should be defined in a config file (see any nf-core module for more information). This greatly helps to parallelize things.

for example:

process CHOPPER {
    tag "Chopper"

    input:
    path reads
    val min_length
    val min_quality

    output:
    path "filtered.fastq", emit: filtered
    path "chopper_stats.txt", emit: stats

would be defined as

process CHOPPER {
    label "process_single"
    tag "${meta.id}"
    input:
       tuple val(meta),path(reads)

    output:
       tuple val(meta),path("*.fastq"), emit: filtered
      tuple val(meta),path("*stats.txt"), emit: stats
script:
    def min_length= task.ext.min_length?:1234
    def min_quality= task.ext.min_quality?:1234
    def prefix =  task.ext.prefix?:"${meta.id}.chopper"
"""
(...)
chopper  (....) > ${prefix}.fastq
(...)
}
`

and in the nextflow_config:

params {
  min_length = 100
  min_quality = 20
  }

process  {
withName: "CHOPPER" {
 ext.min_length = {"${params.min_length}" as int }
ext.min_quality = {"${params.min_quality}" as int }
 }

}

EDIT:

(grep -c "^@" filtered.fastq)

this is a bad way to count the number of records in a fastq file because '@' is a valid quality symbol.

you could use:

cat filtered.fastq | paste - - - - |wc -l