Workflows

These workflows are associated with Pathway analysis with the MINERVA Platform

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\nSample Table"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Cut"];
  0 -->|output| 1;
  2["Select"];
  1 -->|out_file1| 2;
  3["Faster Download and Extract Reads in FASTQ"];
  2 -->|out_file1| 3;
  b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6["Output\noutput_collection"];
  3 --> b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6;
  style b7c7e59d-6a78-41af-ae59-e52fcc1fe2f6 stroke:#2c3143,stroke-width:4px;
	

flowchart TD
  0["ℹ️ Input Collection\nfeatureCounts: Counts"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nfactordata"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nfeatureCounts: Lengths"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Column join"];
  0 -->|output| 3;
  4["Extract dataset"];
  2 -->|output| 4;
  5["countdata"];
  3 -->|tabular_output| 5;
  e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5["Output\ncount_data"];
  5 --> e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5;
  style e8dcfaaf-0d8d-46eb-8cc9-ce2fbdfc45e5 stroke:#2c3143,stroke-width:4px;
  6["annodata"];
  3 -->|tabular_output| 6;
  7["Replace Text"];
  5 -->|outfile| 7;
  8["limma DEG analysis"];
  6 -->|out_tab| 8;
  7 -->|outfile| 8;
  1 -->|output| 8;
  1c8d7950-1003-4c86-9986-c6ed1264cd8b["Output\nlimma_report"];
  8 --> 1c8d7950-1003-4c86-9986-c6ed1264cd8b;
  style 1c8d7950-1003-4c86-9986-c6ed1264cd8b stroke:#2c3143,stroke-width:4px;
  9["Extract dataset"];
  8 -->|outTables| 9;
  10["MINERVA Formatting"];
  9 -->|output| 10;
  9ce4f48b-e742-4b7c-9bde-5d51f11068d3["Output\nminerva_table"];
  10 --> 9ce4f48b-e742-4b7c-9bde-5d51f11068d3;
  style 9ce4f48b-e742-4b7c-9bde-5d51f11068d3 stroke:#2c3143,stroke-width:4px;
  11["Join two Datasets"];
  9 -->|output| 11;
  4 -->|output| 11;
  12["Compute"];
  11 -->|out_file1| 12;
  13["Cut"];
  12 -->|out_file1| 13;
  14["Unique"];
  13 -->|out_file1| 14;
  15["Cut"];
  14 -->|outfile| 15;
  16["Cut"];
  14 -->|outfile| 16;
  17["goseq"];
  15 -->|out_file1| 17;
  16 -->|out_file1| 17;
	

flowchart TD
  0["ℹ️ Input Collection\nmRNA-Seq Reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nUCSC Genome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["FastQC"];
  0 -->|output| 2;
  3["Cutadapt"];
  0 -->|output| 3;
  4["FastQC"];
  3 -->|out1| 4;
  5["HISAT2"];
  3 -->|out1| 5;
  6["featureCounts"];
  5 -->|output_alignments| 6;
  5cb5bd5d-df81-4463-8002-e89551780f01["Output\noutput_feature_lengths"];
  6 --> 5cb5bd5d-df81-4463-8002-e89551780f01;
  style 5cb5bd5d-df81-4463-8002-e89551780f01 stroke:#2c3143,stroke-width:4px;
  5dec13e1-0011-472c-a72d-6715fe55c23c["Output\noutput_short"];
  6 --> 5dec13e1-0011-472c-a72d-6715fe55c23c;
  style 5dec13e1-0011-472c-a72d-6715fe55c23c stroke:#2c3143,stroke-width:4px;
  7["Read Distribution"];
  5 -->|output_alignments| 7;
  1 -->|output| 7;
  8["Gene Body Coverage BAM"];
  5 -->|output_alignments| 8;
  1 -->|output| 8;
  9["Multi QC raw reads"];
  2 -->|text_file| 9;
  4 -->|text_file| 9;
  3 -->|report| 9;
  5 -->|summary_file| 9;
  7 -->|output| 9;
  8 -->|outputtxt| 9;
  6 -->|output_summary| 9;
  9217af4e-e34c-4a49-9d67-4b3df511ac2c["Output\nhtml_report"];
  9 --> 9217af4e-e34c-4a49-9d67-4b3df511ac2c;
  style 9217af4e-e34c-4a49-9d67-4b3df511ac2c stroke:#2c3143,stroke-width:4px;
	

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: