Workflows

These workflows are associated with Automating Galaxy workflows using the command line

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.

vcf2lineage
Wolfgang Maier

Last updated Jun 8, 2021

Launch in Tutorial Mode
License: MIT
Tests: ❌ Results: Not yet automated

Download Galaxy Workflow.ga Galaxy Europe Galaxy Australia Galaxy Main Galaxy France Import to another server (≥23.0+ only!) 
flowchart TD
  0["ℹ️ Input Collection\nVariant calls"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Parameter\nmin-AF for consensus variant"];
  style 1 fill:#ded,stroke:#393,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference genome"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Compose text parameter value"];
  1 -->|output| 3;
  4["SnpSift Filter"];
  3 -->|out1| 4;
  0 -->|output| 4;
  ee67c5ed-ff7c-404b-ad20-19259edbc671["Output\nconsensus_variants"];
  4 --> ee67c5ed-ff7c-404b-ad20-19259edbc671;
  style ee67c5ed-ff7c-404b-ad20-19259edbc671 stroke:#2c3143,stroke-width:4px;
  5["bcftools consensus"];
  4 -->|output| 5;
  2 -->|output| 5;
  9028f80e-4112-40d8-9a49-f671677d304f["Output\nconsensus"];
  5 --> 9028f80e-4112-40d8-9a49-f671677d304f;
  style 9028f80e-4112-40d8-9a49-f671677d304f stroke:#2c3143,stroke-width:4px;
  6["Collapse Collection"];
  5 -->|output_file| 6;
  1dd7978e-b907-42d6-8fc4-f6fadeefcad1["Output\nmultisample_consensus_fasta"];
  6 --> 1dd7978e-b907-42d6-8fc4-f6fadeefcad1;
  style 1dd7978e-b907-42d6-8fc4-f6fadeefcad1 stroke:#2c3143,stroke-width:4px;
  7["Pangolin"];
  6 -->|output| 7;
  e02d2cfb-9842-4069-957c-6cf4ec197056["Output\npangolin_results"];
  7 --> e02d2cfb-9842-4069-957c-6cf4ec197056;
  style e02d2cfb-9842-4069-957c-6cf4ec197056 stroke:#2c3143,stroke-width:4px;

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 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