Workflows

These workflows are associated with Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

flowchart TD
  0["ℹ️ Input Collection\nCollection of paired short-reads data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nCollection of long-reads data"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Samtools fastx"];
  7 -->|outputsam| 10;
  11["Samtools fastx"];
  9 -->|outputsam| 11;
  12["Collapse Collection"];
  10 -->|nonspecific| 12;
  13["Zip Collection"];
  11 -->|forward| 13;
  11 -->|reverse| 13;
  14["Collapse Collection"];
  11 -->|forward| 14;
  15["Collapse Collection"];
  11 -->|reverse| 15;
  16["seqtk_sample"];
  14 -->|output| 16;
  17["seqtk_sample"];
  15 -->|output| 17;
  18["Create assemblies with Unicycler"];
  12 -->|output| 18;
  16 -->|default| 18;
  17 -->|default| 18;
  19["Bandage Info"];
  18 -->|assembly_graph| 19;
  2["fastp: Trimmed Illumina Reads"];
  0 -->|output| 2;
  20["Filter sequences by length"];
  18 -->|assembly| 20;
  21["Bandage Image"];
  18 -->|assembly_graph| 21;
  3["NanoPlot"];
  1 -->|output| 3;
  4["Map with minimap2"];
  1 -->|output| 4;
  5["MultiQC"];
  2 -->|report_json| 5;
  6["Bowtie2"];
  2 -->|output_paired_coll| 6;
  7["Samtools view"];
  4 -->|alignment_output| 7;
  8["Samtools stats"];
  4 -->|alignment_output| 8;
  9["Samtools view"];
  6 -->|output| 9;
	

flowchart TD
  0["ℹ️ Input Dataset\nList of Illumina accessions"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nList of ONT accessions"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Samtools stats"];
  6 -->|alignment_output| 10;
  11["Samtools view"];
  8 -->|output| 11;
  12["Samtools fastx"];
  9 -->|outputsam| 12;
  13["Samtools fastx"];
  11 -->|outputsam| 13;
  14["Collapse Collection"];
  12 -->|nonspecific| 14;
  15["Zip Collection"];
  13 -->|forward| 15;
  13 -->|reverse| 15;
  16["Collapse Collection"];
  13 -->|forward| 16;
  17["Collapse Collection"];
  13 -->|reverse| 17;
  18["seqtk_sample"];
  16 -->|output| 18;
  19["seqtk_sample"];
  17 -->|output| 19;
  2["Illumina data"];
  0 -->|output| 2;
  20["Create assemblies with Unicycler"];
  14 -->|output| 20;
  18 -->|default| 20;
  19 -->|default| 20;
  21["Bandage Info"];
  20 -->|assembly_graph| 21;
  22["Bandage Image"];
  20 -->|assembly_graph| 22;
  23["Filter sequences by length"];
  20 -->|assembly| 23;
  3["ONT data"];
  1 -->|output| 3;
  4["fastp: Trimmed Illumina Reads"];
  2 -->|list_paired| 4;
  5["NanoPlot"];
  3 -->|output_collection| 5;
  6["Map with minimap2"];
  3 -->|output_collection| 6;
  7["MultiQC"];
  4 -->|report_json| 7;
  8["Bowtie2"];
  4 -->|output_paired_coll| 8;
  9["Samtools view"];
  6 -->|alignment_output| 9;
	

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure: