Training Sanger sequences CHD8

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy France
• Galaxy Australia
• Galaxy Main
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nAOPEP_and_CHD8_sequences_20220907.zip?download=1"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nPrim"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Unzip"];
  0 -->|output| 2;
  3["Filter FASTA"];
  1 -->|output| 3;
  4["Filter FASTA"];
  1 -->|output| 4;
  5["Extract element identifiers"];
  2 -->|unzipped| 5;
  6["Degap.seqs"];
  3 -->|output| 6;
  7["Degap.seqs"];
  4 -->|output| 7;
  8["Regex Find And Replace"];
  5 -->|output| 8;
  9["Regex Find And Replace"];
  5 -->|output| 9;
  10["Reverse-Complement"];
  7 -->|out_fasta| 10;
  11["Filter collection"];
  8 -->|out_file1| 11;
  2 -->|unzipped| 11;
  12["Filter collection"];
  9 -->|out_file1| 12;
  11 -->|output_discarded| 12;
  13["ab1 to FASTQ converter"];
  11 -->|output_filtered| 13;
  14["ab1 to FASTQ converter"];
  12 -->|output_filtered| 14;
  15["seqtk_trimfq"];
  13 -->|output| 15;
  16["seqtk_trimfq"];
  14 -->|output| 16;
  17["FASTQ Groomer"];
  15 -->|default| 17;
  18["Sort collection"];
  16 -->|default| 18;
  19["Sort collection"];
  17 -->|output_file| 19;
  20["Reverse-Complement"];
  19 -->|output| 20;
  21["seqtk_mergepe"];
  18 -->|output| 21;
  20 -->|output| 21;
  22["FASTQ Groomer"];
  21 -->|default| 22;
  23["FASTQ to Tabular"];
  22 -->|output_file| 23;
  24["Tabular-to-FASTA"];
  23 -->|output_file| 24;
  25["Align sequences"];
  24 -->|output| 25;
  26["Consensus sequence from aligned FASTA"];
  25 -->|aligned_sequences| 26;
  27["Merge.files"];
  26 -->|output| 27;
  28["Merge.files"];
  27 -->|output| 28;
  10 -->|output| 28;
  6 -->|out_fasta| 28;
  29["Regex Find And Replace"];
  28 -->|output| 29;
  30["Align sequences"];
  29 -->|out_file1| 30;
  31["NCBI BLAST+ blastn"];
  29 -->|out_file1| 31;

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.

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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/Manage_AB1_Sanger/workflows/Training-Sanger-sequences-CHD8.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows