#@UGENE_WORKFLOW
#Reads in FASTQ file produced by CASAVA 1.8 contain 'N' or 'Y' as a part of an idetifier. 'Y' if a read if filtered, 'N' if the read if the read is not filtered. The workflow cleans up the filtered reads.
#For example:
#@HWI-ST880:181:D1WRUACXX:8:1102:4905:2125 1:N:0:TAAGGG
#CTTACATAACTACTGACCATGCTCTCTCTTGTCTGTCTCTTATACACATCT
#+
#111442222322324232AAFFHIJJJJJJIHIIF111CGGFHIG???FGB
#@HWI-ST880:181:D1WRUACXX:8:1102:7303:2101 1:Y:0:TAAGGG
#TCCTTACTGTCTGAGCAATGGGATTCCATCTTTTACGATCTAGACATGGCT
#+
#11++4222322<CEE2<:3<3333333<A<CAFE:1?C??::C?00?BD90

include "CASAVA FASTQ filter.usa" as "Script-CASAVA FASTQ filter"

workflow "CASAVA FASTQ Filter"{

    read-sequence {
        type:read-sequence;
        name:"Read Sequence";
        url-in {
            dataset:"Dataset 1";
        }
    }
    write-sequence {
        type:write-sequence;
        name:"Write Sequence";
        document-format:fastq;
        url-out:fastq.fastq;
    }
    Script-CASAVA-FASTQ-filter {
        type:"Script-CASAVA FASTQ filter";
        name:"CASAVA FASTQ filter";
        script {
var seqName = getName(in_sequence);
if(seqName.search(".* [^:]*:N:[^:]*:") == 0){
out_sequence = in_sequence;
}else{
out_sequence = null;
}
        };
    }

    .actor-bindings {
        read-sequence.out-sequence->Script-CASAVA-FASTQ-filter.in
        Script-CASAVA-FASTQ-filter.out->write-sequence.in-sequence
    }

    read-sequence.annotations->write-sequence.in-sequence.annotations
    Script-CASAVA-FASTQ-filter.sequence->write-sequence.in-sequence.sequence
    read-sequence.sequence->Script-CASAVA-FASTQ-filter.in.sequence

    .meta {
        parameter-aliases {
            read-sequence.url-in {
                alias:in;
            }
            write-sequence.url-out {
                alias:out;
            }
        }
        visual {
            Script-CASAVA-FASTQ-filter {
                pos:"-540 -540";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in.angle:180;
                out.angle:360;
            }
            read-sequence {
                pos:"-750 -540";
                style:ext;
                bg-color-ext:"0 128 128 64";
                out-sequence.angle:360;
            }
            write-sequence {
                pos:"-285 -540";
                style:ext;
                bg-color-ext:"0 128 128 64";
                in-sequence.angle:180;
            }
            Script-CASAVA-FASTQ-filter.out->write-sequence.in-sequence {
                text-pos:"-40.7422 -27";
            }
            read-sequence.out-sequence->Script-CASAVA-FASTQ-filter.in {
                text-pos:"-33.8281 -27";
            }
        }
    }
}