Workflows
These workflows are associated with ERGA post-assembly QC
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.
Post-assembly workflow
Cristóbal Gallardo Alba
Last updated Sep 6, 2024
Launch in Tutorial Mode
License:
AGPL-3.0-or-later
Tests: ✅
Results: Not yet automated
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;
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:
Video: Importing a workflow from URL