#@UGENE_WORKFLOW #The workflow takes FASTQ files (with paired-end sequencing reads) as input and process this data as follows: # - Filters the input sequencing reads by the CASAVA header (for Illumina platform). # - Cuts of adapter sequences. # - Trims the sequencing reads by quality. # - Merges different FASTQ files. # #The workflow also performs quality control of the data with FastQC: first, on the input FASTQ files and, second, after the pre-processing step. # #Besides intermediate files and FastQC reports, the final result of the workflow running is a merged FASTQ file. # workflow "Processing of raw RNA-Seq paired-end reads"{ CASAVAFilter { type:CASAVAFilter; name:"Filter Reads by CASAVA Header"; custom-dir:filtered_fastq; } QualityTrim { type:QualityTrim; name:"Trim Reads by Quality"; custom-dir:filtered_fastq; out-mode:0; len-id:10; qual-id:20; } get-file-list { type:get-file-list; name:"Read FASTQ Files with Reads 1"; url-in { dataset:"Dataset 1"; } } MergeFastq { type:MergeFastq; name:"Merge FASTQ Files"; custom-dir:filtered_fastq; out-mode:0; out-name:in_1.fq; } get-file-list-1 { type:get-file-list; name:"Read FASTQ Files with Reads 2"; url-in { dataset:"Dataset 1"; } } CASAVAFilter-1 { type:CASAVAFilter; name:"Filter Reads by CASAVA Header"; custom-dir:filtered_fastq; } QualityTrim-1 { type:QualityTrim; name:"Trim Reads by Quality"; custom-dir:filtered_fastq; out-mode:0; len-id:10; qual-id:20; } MergeFastq-1 { type:MergeFastq; name:"Merge FASTQ Files"; custom-dir:filtered_fastq; out-mode:0; out-name:in_2.fq; } multiplexer { type:multiplexer; name:Multiplexer; } CutAdaptFastq { type:CutAdaptFastq; name:"Cut Adapter"; out-mode:0; } CutAdaptFastq-1 { type:CutAdaptFastq; name:"Cut Adapter"; out-mode:0; } fastqc { type:fastqc; name:"FastQC Quality Control"; out-mode:1; } fastqc-1 { type:fastqc; name:"FastQC Quality Control"; out-mode:1; } fastqc-1-1 { type:fastqc; name:"FastQC Quality Control"; out-mode:1; } fastqc-1-1-1 { type:fastqc; name:"FastQC Quality Control"; out-mode:1; } .actor-bindings { CASAVAFilter.out-file->CutAdaptFastq-1.in-file QualityTrim.out-file->MergeFastq.in-file get-file-list.out-url->CASAVAFilter.in-file get-file-list.out-url->fastqc.in-file MergeFastq.out-file->multiplexer.input-data-1 MergeFastq.out-file->fastqc-1-1-1.in-file get-file-list-1.out-url->CASAVAFilter-1.in-file get-file-list-1.out-url->fastqc-1.in-file CASAVAFilter-1.out-file->CutAdaptFastq.in-file QualityTrim-1.out-file->MergeFastq-1.in-file MergeFastq-1.out-file->multiplexer.input-data-2 MergeFastq-1.out-file->fastqc-1-1.in-file CutAdaptFastq.out-file->QualityTrim-1.in-file CutAdaptFastq-1.out-file->QualityTrim.in-file } get-file-list.url->CASAVAFilter.in-file.url CutAdaptFastq-1.url->QualityTrim.in-file.url QualityTrim.url->MergeFastq.in-file.url get-file-list-1.url->CASAVAFilter-1.in-file.url CutAdaptFastq.url->QualityTrim-1.in-file.url QualityTrim-1.url->MergeFastq-1.in-file.url CASAVAFilter-1.url->CutAdaptFastq.in-file.url CASAVAFilter.url->CutAdaptFastq-1.in-file.url get-file-list.url->fastqc.in-file.url get-file-list-1.url->fastqc-1.in-file.url MergeFastq-1.url->fastqc-1-1.in-file.url MergeFastq.url->fastqc-1-1-1.in-file.url .meta { parameter-aliases { CASAVAFilter.out-mode { alias:out_mode; } get-file-list.url-in { alias:in; } get-file-list-1.url-in { alias:in_mate; } CASAVAFilter-1.out-mode { alias:out_mode1; } } visual { CASAVAFilter { pos:"-1268 -716"; style:ext; bg-color-ext:"194 0 0 64"; bounds:"-30 -30 123.875 82"; in-file.angle:97.4959; out-file.angle:300.493; } CASAVAFilter-1 { pos:"-786 -1011"; style:ext; bg-color-ext:"194 0 0 64"; bounds:"-30 -30 119.875 70"; in-file.angle:181.79; out-file.angle:359.076; } CutAdaptFastq { pos:"-583 -892"; style:ext; bg-color-ext:"236 177 178 64"; in-file.angle:111.801; out-file.angle:324.713; } CutAdaptFastq-1 { pos:"-1183 -534"; style:ext; bg-color-ext:"236 177 178 64"; in-file.angle:35.7067; out-file.angle:343.951; } MergeFastq { pos:"-662 -329"; style:simple; bg-color-simple:"78 151 184 255"; in-file.angle:171.384; out-file.angle:8.61565; } MergeFastq-1 { pos:"-326 -514"; style:simple; bg-color-simple:"78 151 184 255"; in-file.angle:82.4054; out-file.angle:271.432; } QualityTrim { pos:"-1004 -371"; style:ext; bg-color-ext:"204 68 102 64"; in-file.angle:25.0169; out-file.angle:345.453; } QualityTrim-1 { pos:"-355 -738"; style:ext; bg-color-ext:"204 68 102 64"; bounds:"-30 -30 139.125 84"; in-file.angle:188.13; out-file.angle:289.522; } fastqc { pos:"-1064 -809"; style:simple; bg-color-simple:"0 128 128 255"; in-file.angle:180; } fastqc-1 { pos:"-927 -862"; style:simple; bg-color-simple:"0 128 128 255"; in-file.angle:86.8202; } fastqc-1-1 { pos:"-489 -487"; style:simple; bg-color-simple:"0 128 128 255"; in-file.angle:347.619; } fastqc-1-1-1 { pos:"-627 -487"; style:simple; bg-color-simple:"0 128 128 255"; in-file.angle:273.27; } get-file-list { pos:"-1316 -903"; style:ext; bg-color-ext:"24 102 175 64"; bounds:"-30 -30 79.25 90"; out-url.angle:296.095; } get-file-list-1 { pos:"-1007 -1057"; style:ext; bg-color-ext:"24 102 175 64"; bounds:"-30 -30 75 92"; out-url.angle:328.062; } multiplexer { pos:"-436 -358"; style:simple; bg-color-simple:"84 84 84 255"; input-data-1.angle:220.236; input-data-2.angle:30.6997; output-data.angle:319.574; } CASAVAFilter-1.out-file->CutAdaptFastq.in-file { text-pos:"-15.75 -27"; } CASAVAFilter.out-file->CutAdaptFastq-1.in-file { text-pos:"9.25 -27"; } CutAdaptFastq-1.out-file->QualityTrim.in-file { text-pos:"6.25 10"; } CutAdaptFastq.out-file->QualityTrim-1.in-file { text-pos:"-51.75 -11"; } MergeFastq-1.out-file->fastqc-1-1.in-file { text-pos:"-48.75 -29"; } MergeFastq-1.out-file->multiplexer.input-data-2 { text-pos:"-24.75 -7"; } MergeFastq.out-file->fastqc-1-1-1.in-file { text-pos:"-37.75 -38"; } MergeFastq.out-file->multiplexer.input-data-1 { text-pos:"-36.75 4"; } QualityTrim-1.out-file->MergeFastq-1.in-file { text-pos:"-35.75 -24"; } QualityTrim.out-file->MergeFastq.in-file { text-pos:"-42.75 -38"; } get-file-list-1.out-url->CASAVAFilter-1.in-file { text-pos:"-44.7578 -26"; } get-file-list-1.out-url->fastqc-1.in-file { text-pos:"-40.7578 11"; } get-file-list.out-url->CASAVAFilter.in-file { text-pos:"-48.7578 -17"; } get-file-list.out-url->fastqc.in-file { text-pos:"-32.7578 -28"; } } wizard { name:"Raw RNA-Seq Data Processing Wizard"; help-page-id:16122727; page { id:1; next:2; title:"Input data"; parameters-area { group { title:"Sequencing reads"; label-size:120; get-file-list.url-in { label:"FASTQ files"; } get-file-list-1.url-in { label:"FASTQ files with pairs"; } } } } page { id:2; next:3; title:Pre-processing; parameters-area { group { title:"Reads filtration"; label-size:120; QualityTrim.qual-id { } QualityTrim.len-id { label:"Min length"; } QualityTrim.both-ends { label:"Trim both ends"; } CutAdaptFastq.adapters-url { label:"3' adapters"; } CutAdaptFastq.front-url { label:"5' adapters"; } CutAdaptFastq.anywhere-url { label:"5' and 3' adapters"; } } group { title:"Read pairs filtration"; label-size:120; QualityTrim-1.qual-id { } QualityTrim-1.len-id { label:"Min length"; } QualityTrim-1.both-ends { label:"Trim both ends"; } CutAdaptFastq-1.adapters-url { label:"3' adapters"; } CutAdaptFastq-1.front-url { label:"5' adapters"; } CutAdaptFastq-1.anywhere-url { label:"5' and 3' adapters"; } } } } page { id:3; title:"Output data"; parameters-area { group { title:"Filtered FASTQ"; label-size:130; type:hideable; CASAVAFilter.out-mode { } CASAVAFilter.custom-dir { } } group { title:"Filtered FASTQ with pairs"; label-size:130; type:hideable; CASAVAFilter-1.out-mode { } CASAVAFilter-1.custom-dir { } } } } } } }