flowchart TD
0["ℹ️ Input Collection\nSingle-End FASTQs"];
style 0 stroke:#2c3143,stroke-width:4px;
1["ℹ️ Input Collection\nPaired-End FASTQs"];
style 1 stroke:#2c3143,stroke-width:4px;
2["ℹ️ Input Dataset\nMycobacterium_tuberculosis_ancestral_reference.gbk"];
style 2 stroke:#2c3143,stroke-width:4px;
3["Trimmomatic"];
0 -->|output| 3;
4["Trimmomatic"];
1 -->|output| 4;
5["Mapping and variant calling of SINGLE END FASTQs with snippy"];
3 -->|fastq_out| 5;
2 -->|output| 5;
6["Mapping and variant calling of PAIRED END FASTQs with snippy"];
4 -->|fastq_out_paired| 6;
2 -->|output| 6;
7["Merge PE/SE VCFs in a single collection with all samples"];
5 -->|snpvcf| 7;
6 -->|snpvcf| 7;
8["Merge PE/SE BAMs in a single collection with all samples Part the workflow ”Identifying DR with TB-profiler"];
5 -->|snpsbam| 8;
6 -->|snpsbam| 8;
9["TB Variant Filter"];
7 -->|output| 9;
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
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-uploadImport 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:
Download Workflow RO-Crate
View on WorkflowHub