Workflows

These workflows are associated with 16S Microbial Analysis with mothur (short)

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 Dataset\nContigs"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nGroups"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Summary.seqs"];
  0 -->|output| 2;
  3["Screen.seqs"];
  0 -->|output| 3;
  1 -->|output| 3;
  4["Summary.seqs"];
  3 -->|fasta_out| 4;
  5["Unique.seqs"];
  3 -->|fasta_out| 5;
  6["Count.seqs"];
  3 -->|groups_out| 6;
  5 -->|out_names| 6;
	

flowchart TD
  0["ℹ️ Input Dataset\nAligned Sequences"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nCount Table"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Summary.seqs"];
  1 -->|output| 2;
  0 -->|output| 2;
  3["Screen.seqs"];
  1 -->|output| 3;
  0 -->|output| 3;
  4["Filter.seqs"];
  3 -->|fasta_out| 4;
  5["Unique.seqs"];
  4 -->|filteredfasta| 5;
  3 -->|count_out| 5;
  6["Pre.cluster"];
  5 -->|out_fasta| 6;
  5 -->|out_count| 6;
  7["Summary.seqs"];
  6 -->|count_out| 7;
  6 -->|fasta_out| 7;
  a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d["Output\nSummary.seqs on input dataset(s): summary"];
  7 --> a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d;
  style a0bbcba1-40f9-4678-9c47-8bdb4e0b7f6d stroke:#2c3143,stroke-width:4px;
  8["Chimera.vsearch"];
  6 -->|fasta_out| 8;
  6 -->|count_out| 8;
  9["Remove.seqs"];
  8 -->|out_accnos| 9;
  8 -->|out_count| 9;
  6 -->|fasta_out| 9;
  10["Summary.seqs"];
  9 -->|count_out| 10;
  9 -->|fasta_out| 10;
	

flowchart TD
  0["ℹ️ Input Dataset\nCleaned Sequences"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nCount Table"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nTraining set FASTA"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nTraining set Taxonomy"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Classify.seqs"];
  2 -->|output| 4;
  1 -->|output| 4;
  0 -->|output| 4;
  3 -->|output| 4;
  5["Remove.lineage"];
  1 -->|output| 5;
  0 -->|output| 5;
  4 -->|taxonomy_out| 5;
  6["Summary.seqs"];
  5 -->|count_out| 6;
  5 -->|fasta_out| 6;
	

flowchart TD
  0["ℹ️ Input Dataset\nMock Count Table"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nMock Sequences"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Dist.seqs"];
  1 -->|output| 2;
  3["Cluster"];
  0 -->|output| 3;
  2 -->|out_dist| 3;
  4["Make.shared"];
  0 -->|output| 4;
  3 -->|otulist| 4;
  5["Rarefaction.single"];
  4 -->|shared| 5;
	

flowchart TD
  0["ℹ️ Input Dataset\nSequences"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nCount Table"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nTaxonomy"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Remove.groups"];
  0 -->|output| 3;
  1 -->|output| 3;
  2 -->|output| 3;
  4["Cluster.split"];
  3 -->|fasta_out| 4;
  3 -->|count_out| 4;
  3 -->|taxonomy_out| 4;
  5["Make.shared"];
  3 -->|count_out| 5;
  4 -->|otulist| 5;
  6["Classify.otu"];
  3 -->|count_out| 6;
  4 -->|otulist| 6;
  3 -->|taxonomy_out| 6;
  7["Count.groups"];
  5 -->|shared| 7;
  8["Sub.sample"];
  5 -->|shared| 8;
	

flowchart TD
  0["ℹ️ Input Dataset\nShared file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Rarefaction.single"];
  0 -->|output| 1;
  2["Summary.single"];
  0 -->|output| 2;
  3["Plotting tool"];
  1 -->|rarefactioncurves| 3;
	

flowchart TD
  0["ℹ️ Input Dataset\nShared file from Make.shared"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nSub.sample shared"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Dist.shared"];
  0 -->|output| 2;
  3["Collapse Collection"];
  1 -->|output| 3;
  4["Heatmap.sim"];
  2 -->|distfiles| 4;
  5["Tree.shared"];
  2 -->|distfiles| 5;
  6["Venn"];
  3 -->|output| 6;
  7["Newick Display"];
  5 -->|tre| 7;
	

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: