Workflows

These workflows are associated with Differential abundance testing of small RNAs

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.

sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming)

Last updated Jan 15, 2020

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

flowchart TD
  0["ℹ️ Input Collection\nInput dataset collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nrRNA reference FASTA"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nmiRNA hairpin reference FASTA"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["FastQC"];
  0 -->|output| 3;
  4["Trim Galore!"];
  0 -->|output| 4;
  5["FastQC"];
  4 -->|trimmed_reads_single| 5;
  6["HISAT"];
  4 -->|trimmed_reads_single| 6;
  1 -->|output| 6;
  7["Filter SAM or BAM, output SAM or BAM"];
  6 -->|output_alignments| 7;
  8["Convert from BAM to FastQ"];
  7 -->|output1| 8;
  9["HISAT"];
  8 -->|output| 9;
  2 -->|output| 9;
  10["Filter SAM or BAM, output SAM or BAM"];
  9 -->|output_alignments| 10;
  11["Convert from BAM to FastQ"];
  10 -->|output1| 11;
  12["Manipulate FASTQ"];
  11 -->|output| 12;
  13["Manipulate FASTQ"];
  11 -->|output| 13;
  14["FastQC"];
  12 -->|output_file| 14;
  15["FastQC"];
  13 -->|output_file| 15;

sRNA Seq Step 2: Salmon And DESeq2

Last updated Jan 15, 2020

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

flowchart TD
  0["ℹ️ Input Collection\nDataset collection - Control"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nDataset - Ref Txome"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Collection\nDataset collection - Case"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nInput dataset"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Salmon"];
  1 -->|output| 4;
  0 -->|output| 4;
  5["Salmon"];
  1 -->|output| 5;
  0 -->|output| 5;
  6["Salmon"];
  1 -->|output| 6;
  2 -->|output| 6;
  7["Salmon"];
  1 -->|output| 7;
  2 -->|output| 7;
  8["DESeq2"];
  6 -->|output_quant| 8;
  4 -->|output_quant| 8;
  3 -->|output| 8;
  9["DESeq2"];
  7 -->|output_quant| 9;
  5 -->|output_quant| 9;
  3 -->|output| 9;
  10["Filter"];
  8 -->|deseq_out| 10;
  11["Filter"];
  9 -->|deseq_out| 11;

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: