process trim_galore {
    tag "$sample_id"
    publishDir "${params.outdir}/trim_galore", mode: 'copy',
        saveAs: {filename ->
            if (filename.indexOf("_fastqc") > 0) "FastQC/$filename"
            else if (filename.indexOf("trimming_report.txt") > 0) "logs/$filename"
            else filename
        }

    container 'quay.io/biocontainers/trim-galore:0.6.5--0'

    input:
    tuple sample_id, path(reads)

    output:
    tuple name, path("*fq.gz")
    path "*trimming_report.txt"
    path "*_fastqc.{zip,html}"

    script:
    c_r1 = clip_r1 > 0 ? "--clip_r1 ${clip_r1}" : ''
    c_r2 = clip_r2 > 0 ? "--clip_r2 ${clip_r2}" : ''
    tpc_r1 = three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${three_prime_clip_r1}" : ''
    tpc_r2 = three_prime_clip_r2 > 0 ? "--three_prime_clip_r2 ${three_prime_clip_r2}" : ''
    nextseq = params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : ''
    if (params.singleEnd) {
        """
        trim_galore --fastqc --gzip $c_r1 $tpc_r1 $nextseq $reads
        """
    } else {
        """
        trim_galore --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq $reads
        """
    }
}