trimReads.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include {
    getInputFastqs;
} from "${projectDir}/modules/alignmentPipeline.nf"

include {
    getNpAdapter;
    getT3uAdapter;
    getT2pAdapter;
    getT3pAdapter;
    getT2sAdapter;
    getT3sAdapter;
    trimgalore;
    trimmomatic;
} from "${projectDir}/modules/getReadsQualityReports.nf"

workflow {
    println "\nFastq trimming begins here\n"
    fastq = getInputFastqs()

    if(params.trimmer.toUpperCase() == 'TRIMMOMATIC') {

        if(params.adapter.toUpperCase() == "NP") {
            adapter = getNpAdapter()
            fastq
                .combine(adapter)
                .set { trim_input }
        }
        else if(params.adapter.toUpperCase() == "T3U") {
            adapter = getT3uAdapter()
            fastq
                .combine(adapter)
                .set { trim_input }
        }
        else if(params.adapter.toUpperCase() == "T2P") {
            adapter = getT2pAdapter()
            fastq
                .combine(adapter)
                .set { trim_input }
        }
        else if(params.adapter.toUpperCase() == "T3P") {
            adapter = getT3pAdapter()
            fastq
                .combine(adapter)
                .set { trim_input }
        }
        else if(params.adapter.toUpperCase() == "T2S") {
            adapter = getT2sAdapter()
            fastq
                .combine(adapter)
                .set { trim_input }
        }
        else if(params.adapter.toUpperCase() == "T3S") {
            adapter = getT3sAdapter()
            fastq
                .combine(adapter)
                .set { trim_input }
        }
        else {
            error: println """
        Please select and adapter!
        --------------------------
        Options:
            NP   --> NexteraPE-PE.fa
            T3U  --> TruSeq3-PE-2.fa [Illumina universal]
            T2P  --> TruSeq2-PE.fa
            T2S  --> TruSeq2-SE.fa
            T3P  --> TruSeq3-PE.fa
            T3S  --> TruSeq3-SE.fa
    
        Edit the config file or use '--adapter NP' on the command line
        """
        }
    
        trimmed_reads = trimmomatic(trim_input)

    }
    else {
        trimmed = trimgalore(fastq)
    }

}