Workflows

These workflows are associated with Analyses of metagenomics data - The global picture

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.

Amplicon Tutorial

Last updated Jan 11, 2024

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ✅ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nSILVA Reference"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nAnguil Soil Sample"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPampa Soil Sample"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nTrainset PDS alignment"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nTrainset PDS taxonomy"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Merge.files"];
  2 -->|output| 5;
  1 -->|output| 5;
  6["Make.group"];
  1 -->|output| 6;
  2 -->|output| 6;
  7["Unique.seqs"];
  5 -->|output| 7;
  8["Count.seqs"];
  6 -->|output| 8;
  7 -->|out_names| 8;
  9["Summary.seqs"];
  8 -->|seq_count| 9;
  7 -->|out_fasta| 9;
  10["Screen.seqs"];
  7 -->|out_fasta| 10;
  8 -->|seq_count| 10;
  11["Align.seqs"];
  0 -->|output| 11;
  10 -->|fasta_out| 11;
  12["Summary.seqs"];
  10 -->|count_out| 12;
  11 -->|out_file| 12;
  13["Screen.seqs"];
  11 -->|out_file| 13;
  10 -->|count_out| 13;
  14["Filter.seqs"];
  13 -->|fasta_out| 14;
  15["Pre.cluster"];
  14 -->|filteredfasta| 15;
  13 -->|count_out| 15;
  16["Classify.seqs"];
  15 -->|count_out| 16;
  3 -->|output| 16;
  15 -->|fasta_out| 16;
  4 -->|output| 16;
  17["Cluster.split"];
  16 -->|taxonomy_out| 17;
  15 -->|fasta_out| 17;
  15 -->|count_out| 17;
  18["Make.shared"];
  15 -->|count_out| 18;
  17 -->|otulist| 18;
  5189f9d9-9c06-4547-b255-747e7c54a87b["Output\nmothur_make_shared_shared"];
  18 --> 5189f9d9-9c06-4547-b255-747e7c54a87b;
  style 5189f9d9-9c06-4547-b255-747e7c54a87b stroke:#2c3143,stroke-width:4px;
  19["Classify.otu"];
  15 -->|count_out| 19;
  16 -->|taxonomy_out| 19;
  17 -->|otulist| 19;
  20["Make.biom"];
  18 -->|shared| 20;
  19 -->|taxonomies| 20;
  21["Visualize  with Krona"];
  19 -->|taxonomies| 21;
	
WGS Part In "Analyses Of Metagenomics Data - The Global Picture"

Last updated Jan 11, 2024

Launch in Tutorial Mode question
License: None Specified, defaults to CC-BY-4.0
Tests: ❌ Results: Not yet automated

flowchart TD
  0["ℹ️ Input Dataset\nInput dataset"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["MetaPhlAn2"];
  0 -->|output| 1;
  2["Format MetaPhlAn2"];
  1 -->|output_file| 2;
  3["HUMAnN2"];
  0 -->|output| 3;
  1 -->|output_file| 3;
  4["Krona pie chart"];
  2 -->|krona| 4;
  5["Renormalize"];
  3 -->|gene_families_tsv| 5;
  6["Regroup"];
  3 -->|gene_families_tsv| 6;
  7["Renormalize"];
  6 -->|output_table| 7;
	

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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: