Workflows

These workflows are associated with Essential genes detection with Transposon insertion sequencing

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.

Essential genes detection with Transposon insertion sequencing

Last updated Oct 18, 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 Dataset\nTnseq-Tutorial-reads.fastqsanger.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncondition_barcodes.fasta"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nconstruct_barcodes.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nstaph_aur.fasta"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nstaph_aur.gff3"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Cutadapt"];
  0 -->|output| 5;
  1 -->|output| 5;
  6["Nucleotide subsequence search"];
  3 -->|output| 6;
  7["Convert GFF3"];
  4 -->|output| 7;
  8["Cutadapt"];
  5 -->|split_output| 8;
  9["Cut"];
  6 -->|output| 9;
  10["Cut"];
  6 -->|output| 10;
  11["Cutadapt"];
  8 -->|out1| 11;
  12["Compute"];
  10 -->|out_file1| 12;
  13["Cutadapt"];
  11 -->|out1| 13;
  2 -->|output| 13;
  14["Cut"];
  12 -->|out_file1| 14;
  15["Cutadapt"];
  13 -->|split_output| 15;
  16["Map with Bowtie for Illumina"];
  3 -->|output| 16;
  15 -->|out1| 16;
  17["bamCoverage"];
  16 -->|output| 17;
  18["Join"];
  17 -->|outFileName| 18;
  9 -->|out_file1| 18;
  19["Join"];
  17 -->|outFileName| 19;
  14 -->|out_file1| 19;
  20["Cut"];
  18 -->|output| 20;
  21["Cut"];
  19 -->|output| 21;
  22["Sort"];
  20 -->|out_file1| 22;
  23["Compute"];
  21 -->|out_file1| 23;
  24["Cut"];
  23 -->|out_file1| 24;
  25["Sort"];
  24 -->|out_file1| 25;
  26["Join"];
  22 -->|outfile| 26;
  25 -->|outfile| 26;
  27["Compute"];
  26 -->|output| 27;
  28["Cut"];
  27 -->|out_file1| 28;
  29["Sort"];
  28 -->|out_file1| 29;
  30["Gumbel"];
  7 -->|output| 30;
  29 -->|outfile| 30;
  31["Filter"];
  30 -->|sites| 31;
  32["Extract Dataset"];
  31 -->|out_file1| 32;
  8796f62f-4676-4ad2-b085-7597f894c32c["Output\ncontrol"];
  32 --> 8796f62f-4676-4ad2-b085-7597f894c32c;
  style 8796f62f-4676-4ad2-b085-7597f894c32c stroke:#2c3143,stroke-width:4px;
  33["Extract Dataset"];
  31 -->|out_file1| 33;
  bd014de4-708e-419c-bd1e-8bf350661aad["Output\ncondition"];
  33 --> bd014de4-708e-419c-bd1e-8bf350661aad;
  style bd014de4-708e-419c-bd1e-8bf350661aad stroke:#2c3143,stroke-width:4px;
  34["Join"];
  32 -->|output| 34;
  33 -->|output| 34;
  5cdfb5c9-c677-41dc-a838-c4a61d62f5be["Output\nessential_both"];
  34 --> 5cdfb5c9-c677-41dc-a838-c4a61d62f5be;
  style 5cdfb5c9-c677-41dc-a838-c4a61d62f5be stroke:#2c3143,stroke-width:4px;
  35["Join"];
  32 -->|output| 35;
  33 -->|output| 35;
  8b2b65ea-37c3-43d2-b416-38f8f920fbd9["Output\nessential_control"];
  35 --> 8b2b65ea-37c3-43d2-b416-38f8f920fbd9;
  style 8b2b65ea-37c3-43d2-b416-38f8f920fbd9 stroke:#2c3143,stroke-width:4px;
  36["Join"];
  32 -->|output| 36;
  33 -->|output| 36;
  37639319-b053-4fbc-bf61-fd3e38263502["Output\nessential_condition"];
  36 --> 37639319-b053-4fbc-bf61-fd3e38263502;
  style 37639319-b053-4fbc-bf61-fd3e38263502 stroke:#2c3143,stroke-width:4px;
	

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: