vcf2lineage 1.0
Visit source
Download RO-Crate
Run on Galaxyworkflow-automation
Associated Tutorial
This workflows is part of the tutorial Automating Galaxy workflows using the command line, available in the GTN
Thanks to...
Workflow Author(s): Wolfgang Maier
Tutorial Author(s): Simon Bray, Wolfgang Maier
Tutorial Contributor(s): Helena Rasche, Saskia Hiltemann, Wolfgang Maier, Bérénice Batut, Martin Čech, Björn Grüning, Armin Dadras
Funder(s): ELIXIR Europe, de.NBI, University of Freiburg
Grants(s): EuroScienceGateway
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Reference genome | #main/Reference genome | n/a |
|
| Variant calls | #main/Variant calls | n/a |
|
| min-AF for consensus variant | #main/min-AF for consensus variant | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
| 4 | SnpSift Filter | toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/4.3+t.galaxy1 |
| 5 | bcftools consensus | toolshed.g2.bx.psu.edu/repos/iuc/bcftools_consensus/bcftools_consensus/1.10 |
| 6 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 7 | Pangolin | toolshed.g2.bx.psu.edu/repos/iuc/pangolin/pangolin/2.3.8 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| consensus | #main/consensus | n/a |
|
| consensus_variants | #main/consensus_variants | n/a |
|
| multisample_consensus_fasta | #main/multisample_consensus_fasta | n/a |
|
| pangolin_results | #main/pangolin_results | n/a |
|
Version History
master
Creators and Submitter
Views: 1242 Downloads: 180 Runs: 0
Created: 2nd Jun 2025 at 10:51
AttributionsNone
Related items
Teams: Galaxy Training Network
Organizations: Galaxy
I'm a bot managed by @hexylena to upload workflows from the Galaxy Training Network to the WorkflowHub. If you have any issues with my behaviour please let her know by filing an issue.
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy can run ...
Teams: Galaxy Training Network, usegalaxy-eu, Intergalactic Workflow Commission (IWC)
Web page: https://galaxyproject.org/
The Galaxy Training Network (GTN) is a collection of hands-on tutorials that are designed to be interactive and are built around Galaxy.
These tutorials can be used for learning and teaching how to use Galaxy for general data analysis, as well as a wide array of hands-on tutorials covering specific domains such as assembly, RNA-Seq analysis, deep learning, climate analysis, and more!
