#@UGENE_WORKFLOW
workflow "De novo assembly with SPAdes" {
.meta {
wizard {
auto-run: true;
has-run-button: false;
has-defaults-button: false;
name: "Configure De Novo Assembly Workflow";
finish-label: "Setup";
result {
NGS/ngs_assembly_illumina_pe.uwl: "sample_workflow.illumina_pe";
NGS/ngs_assembly_illumina_se.uwl: "sample_workflow.illumina_se";
NGS/ngs_assembly_illumina_pe_nanopore.uwl: "sample_workflow.illumina_pe_nanopore";
}
page {
id: 1;
title: "De novo assembly with SPAdes"
parameters-area {
label {
text:"In general, SPAdes needs at least one library of the following types:
- Illumina paired-end/high-quality mate-pairs/unpaired reads
- IonTorrent paired-end/high-quality mate-pairs/unpaired reads
- PacBio CCS reads
Additionally, one can provide PacBio CLR, Oxford Nanopore, Sanger reads or contigs.";
background-color:"rgb(225,225,225)";
}
group {
title:"Use a sample workflows or create a custom one from it"
radio {
id: sample_workflow
value {
id: illumina_pe;
label: "Illumina PE reads";
tooltip:"Improve Illumina paired-end reads quality with Trimmomatic, assemble them with SPAdes.";
}
value {
id: illumina_se;
label: "Illumina SE reads";
tooltip:"Improve Illumina unpaired (single-end) reads quality with Trimmomatic, assemble them with SPAdes.";
}
value {
id: illumina_pe_nanopore;
label: "Illumina PE and Nanopore reads"
tooltip:"Assemble de novo Illumina paired-end and Oxford Nanopore reads.";
}
}
}
}
}
}
}
}