Workflows

These workflows are associated with RAD-Seq Reference-based data analysis

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\nEBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nhttps://zenodo.org/record/1134547/files/Barcode_SRR034310.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["FastQC"];
  5 -->|demultiplexed| 10;
  11["Map with BWA"];
  5 -->|demultiplexed| 11;
  3 -->|output| 11;
  12["Select"];
  6 -->|output_log| 12;
  13["Select"];
  6 -->|output_log| 13;
  14["Replace Text"];
  7 -->|outfile| 14;
  15["Replace Text"];
  8 -->|out_file1| 15;
  16["Replace Text"];
  9 -->|out_file1| 16;
  17["MultiQC"];
  10 -->|text_file| 17;
  18["Replace Text"];
  12 -->|out_file1| 18;
  19["Replace Text"];
  13 -->|out_file1| 19;
  2["ℹ️ Input Dataset\nhttps://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt"];
  style 2 stroke:#2c3143,stroke-width:4px;
  20["Add column"];
  14 -->|outfile| 20;
  21["Concatenate datasets"];
  19 -->|outfile| 21;
  15 -->|outfile| 21;
  16 -->|outfile| 21;
  18 -->|outfile| 21;
  22["Cut"];
  20 -->|out_file1| 22;
  23["Convert"];
  21 -->|out_file1| 23;
  24["Regex Replace"];
  22 -->|out_file1| 24;
  25["Stacks: reference map"];
  11 -->|bam_output| 25;
  24 -->|outfile| 25;
  26["Stacks: populations"];
  25 -->|all_output| 26;
  24 -->|outfile| 26;
  27["Summary Statistics"];
  26 -->|out_fstats| 27;
  28["Sort"];
  26 -->|out_fstats| 28;
  29["Count"];
  26 -->|out_fstats| 29;
  3["ℹ️ Input Dataset\nhttps://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta"];
  style 3 stroke:#2c3143,stroke-width:4px;
  30["Filter"];
  26 -->|out_fstats| 30;
  4["Stacks: process radtags"];
  1 -->|output| 4;
  0 -->|output| 4;
  5["Stacks: process radtags"];
  1 -->|output| 5;
  0 -->|output| 5;
  6["Stacks: process radtags"];
  1 -->|output| 6;
  0 -->|output| 6;
  7["Replace Text"];
  2 -->|output| 7;
  8["Select"];
  4 -->|output_log| 8;
  9["Select"];
  5 -->|output_log| 9;
	

flowchart TD
  0["ℹ️ Input Dataset\nref_genome_chromFa.tar"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nPopulation_map.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nBarcodes_SRR034310.tabular"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nSRR034310.fastq"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["Stacks: process radtags"];
  2 -->|output| 4;
  3 -->|output| 4;
  5["Stacks: process radtags"];
  2 -->|output| 5;
  3 -->|output| 5;
  6["Stacks: process radtags"];
  2 -->|output| 6;
  3 -->|output| 6;
  7["Map with BWA for Illumina"];
  0 -->|output| 7;
  4 -->|demultiplexed| 7;
  8["Stacks: reference map"];
  7 -->|output| 8;
  1 -->|output| 8;
  9["Stacks: populations"];
  8 -->|all_output| 9;
  1 -->|output| 9;
	

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: