Post-assembly workflow

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nMetadata file"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nNCBI taxonomic ID"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Dataset\nNCBI taxdump directory"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Collection\nLong-read FASTQ files"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nPrimary genome assembly file fasta"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Parameter\nPloidy for model to use"];
  style 5 fill:#ded,stroke:#393,stroke-width:4px;
  6["ℹ️ Input Dataset\nDIAMOND database"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Collection\nHi-C reverse"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Collection\nHi-C forward"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["Meryl"];
  3 -->|output| 9;
  10["Collapse Collection"];
  3 -->|output| 10;
  11["Create BlobtoolKit"];
  4 -->|output| 11;
  0 -->|output| 11;
  2 -->|output| 11;
  1 -->|output| 11;
  12["gfastats"];
  4 -->|output| 12;
  13["Convert compressed file to uncompressed."];
  4 -->|output| 13;
  14["gfastats"];
  4 -->|output| 14;
  15["Diamond"];
  4 -->|output| 15;
  6 -->|output| 15;
  16["Collapse Collection"];
  7 -->|output| 16;
  17["Collapse Collection"];
  8 -->|output| 17;
  18["Meryl"];
  9 -->|read_db| 18;
  19["Map with minimap2"];
  10 -->|output| 19;
  4 -->|output| 19;
  20["Smudgeplot"];
  10 -->|output| 20;
  21["Replace"];
  13 -->|output1| 21;
  22["Bandage Image"];
  14 -->|output| 22;
  23["BWA-MEM2"];
  16 -->|output| 23;
  4 -->|output| 23;
  24["BWA-MEM2"];
  17 -->|output| 24;
  4 -->|output| 24;
  25["Merqury"];
  4 -->|output| 25;
  18 -->|read_db| 25;
  d2dbf498-5155-43b2-bf2a-ffed5c45100d["Output\nMerqury on input dataset(s): stats"];
  25 --> d2dbf498-5155-43b2-bf2a-ffed5c45100d;
  style d2dbf498-5155-43b2-bf2a-ffed5c45100d stroke:#2c3143,stroke-width:4px;
  0b43d206-253f-4c0b-a1f4-971402851c6d["Output\nMerqury on input dataset(s): plots"];
  25 --> 0b43d206-253f-4c0b-a1f4-971402851c6d;
  style 0b43d206-253f-4c0b-a1f4-971402851c6d stroke:#2c3143,stroke-width:4px;
  811a77e8-eb99-4dc7-9295-f0000fcb9fe5["Output\nMerqury on input dataset(s): QV stats"];
  25 --> 811a77e8-eb99-4dc7-9295-f0000fcb9fe5;
  style 811a77e8-eb99-4dc7-9295-f0000fcb9fe5 stroke:#2c3143,stroke-width:4px;
  26["Meryl"];
  18 -->|read_db| 26;
  27["Samtools stats"];
  19 -->|alignment_output| 27;
  28["Busco"];
  21 -->|outfile| 28;
  af98aae6-f1a3-493c-9cef-08e0926210d3["Output\nBusco on input dataset(s): full table"];
  28 --> af98aae6-f1a3-493c-9cef-08e0926210d3;
  style af98aae6-f1a3-493c-9cef-08e0926210d3 stroke:#2c3143,stroke-width:4px;
  929439b7-c688-45ea-848a-97c13d3e0028["Output\nBusco on input dataset(s): short summary"];
  28 --> 929439b7-c688-45ea-848a-97c13d3e0028;
  style 929439b7-c688-45ea-848a-97c13d3e0028 stroke:#2c3143,stroke-width:4px;
  29["Filter and merge"];
  24 -->|bam_output| 29;
  23 -->|bam_output| 29;
  30["Merqury plot 2"];
  25 -->|png_files| 30;
  31["Merqury plot 1"];
  25 -->|png_files| 31;
  32["Merqury plot 3"];
  25 -->|png_files| 32;
  33["Merqury plot 5"];
  25 -->|png_files| 33;
  34["Merqury plot 4"];
  25 -->|png_files| 34;
  35["GenomeScope"];
  26 -->|read_db_hist| 35;
  5 -->|output| 35;
  36["BlobToolKit"];
  15 -->|blast_tabular| 36;
  11 -->|blobdir| 36;
  28 -->|busco_table| 36;
  19 -->|alignment_output| 36;
  37["PretextMap"];
  29 -->|outfile| 37;
  38["BlobToolKit"];
  36 -->|blobdir| 38;
  39["BlobToolKit"];
  36 -->|blobdir| 39;
  40["BlobToolKit"];
  36 -->|blobdir| 40;
  41["Pretext Snapshot"];
  37 -->|pretext_map_out| 41;

Inputs

Outputs

Tools

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/assembly/tutorials/ERGA-post-assembly-QC/workflows/main_workflow.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