Workflows

These workflows are associated with Clean and manage Sanger sequences from raw files to aligned consensus

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 Collection\nL sequences Forward"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nH sequences Reverse"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nLCOI primers"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nHCOI primers"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ab1 to FASTQ converter"];
  0 -->|output| 4;
  5["ab1 to FASTQ converter"];
  1 -->|output| 5;
  6["What’s your LCOI primer sequence identifier ?"];
  2 -->|output| 6;
  7["What’s your HCOI primer sequence identifier ?"];
  3 -->|output| 7;
  8["seqtk_trimfq"];
  4 -->|output| 8;
  9["seqtk_trimfq"];
  5 -->|output| 9;
  10["Degap.seqs"];
  6 -->|output| 10;
  11["Degap.seqs"];
  7 -->|output| 11;
  12["Sort collection"];
  8 -->|default| 12;
  13["FASTQ Groomer"];
  9 -->|default| 13;
  14["Reverse-Complement"];
  11 -->|out_fasta| 14;
  15["Reverse-Complement"];
  13 -->|output_file| 15;
  16["Sort collection"];
  15 -->|output| 16;
  17["seqtk_mergepe"];
  12 -->|output| 17;
  16 -->|output| 17;
  18["FASTQ Groomer"];
  17 -->|default| 18;
  19["FASTQ to Tabular"];
  18 -->|output_file| 19;
  20["Tabular-to-FASTA"];
  19 -->|output_file| 20;
  21["Align sequences"];
  20 -->|output| 21;
  22["Consensus sequence from aligned FASTA"];
  21 -->|aligned_sequences| 22;
  23["Merge.files"];
  22 -->|output| 23;
  24["Merge.files"];
  23 -->|output| 24;
  14 -->|output| 24;
  10 -->|out_fasta| 24;
  25["Regex Find And Replace"];
  24 -->|output| 25;
  26["Align sequences"];
  25 -->|out_file1| 26;
  27["NCBI BLAST+ blastn"];
  25 -->|out_file1| 27;
  31c2dd1a-918e-4648-a407-d0e3d7172253["Output\nw_blast_output"];
  27 --> 31c2dd1a-918e-4648-a407-d0e3d7172253;
  style 31c2dd1a-918e-4648-a407-d0e3d7172253 stroke:#2c3143,stroke-width:4px;
  7514514f-809a-4a14-8981-cb08c950b523["Output\nw_consensus_aligned_sequences"];
  27 --> 7514514f-809a-4a14-8981-cb08c950b523;
  style 7514514f-809a-4a14-8981-cb08c950b523 stroke:#2c3143,stroke-width:4px;
	

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;
	

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: