assembly_with_preprocessing_and_sra_download

Run Workflow in Galaxy

• Galaxy France
• Galaxy Main
• Galaxy Europe
• Galaxy Australia
• Import to another server (≥23.0+ only!)

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;

Inputs

Outputs

Tools

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.

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing_and_sra_download.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows