Workflows
These workflows are associated with Mapping
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.
GTN - Sequence Analyses - Mapping - Jbrowse (imported from uploaded file)
Last updated Apr 21, 2021
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ❌
Results: Not yet automated
flowchart TD 0["ℹ️ Input Dataset\nreads_1"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nreads_2"]; style 1 stroke:#2c3143,stroke-width:4px; 2["FastQC"]; 0 -->|output| 2; 3["FastQC"]; 1 -->|output| 3; 4["Trim Galore!"]; 0 -->|output| 4; 1 -->|output| 4; 5["MultiQC"]; 3 -->|text_file| 5; 2 -->|text_file| 5; 6["Bowtie2"]; 4 -->|trimmed_reads_pair1| 6; 4 -->|trimmed_reads_pair2| 6; cb22563a-fece-4b63-9d85-ff5817edb5c3["Output\nbowtie2_mapping_stats"]; 6 --> cb22563a-fece-4b63-9d85-ff5817edb5c3; style cb22563a-fece-4b63-9d85-ff5817edb5c3 stroke:#2c3143,stroke-width:4px; 7["Samtools stats"]; 6 -->|output| 7; 490620d4-f083-4999-bb33-73a2a1f736b4["Output\nbam_stats_1"]; 7 --> 490620d4-f083-4999-bb33-73a2a1f736b4; style 490620d4-f083-4999-bb33-73a2a1f736b4 stroke:#2c3143,stroke-width:4px; 8["JBrowse"]; 6 -->|output| 8;
GTN - Sequence Analyses - Mapping (imported from uploaded file)
Last updated Apr 21, 2021
Launch in Tutorial Mode
License:
None Specified, defaults to
CC-BY-4.0
Tests: ✅
Results:
flowchart TD 0["ℹ️ Input Dataset\nreads_1"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nreads_2"]; style 1 stroke:#2c3143,stroke-width:4px; 2["FastQC"]; 0 -->|output| 2; 3["FastQC"]; 1 -->|output| 3; 4["Trim Galore!"]; 0 -->|output| 4; 1 -->|output| 4; 5["MultiQC"]; 3 -->|text_file| 5; 2 -->|text_file| 5; 6["Bowtie2"]; 4 -->|trimmed_reads_pair1| 6; 4 -->|trimmed_reads_pair2| 6; d2674912-28a6-45f3-ac48-6635eabe47b7["Output\nbowtie2_mapping_stats"]; 6 --> d2674912-28a6-45f3-ac48-6635eabe47b7; style d2674912-28a6-45f3-ac48-6635eabe47b7 stroke:#2c3143,stroke-width:4px; 7["Stats"]; 6 -->|output| 7; 96de3c0c-4d7e-423b-8e9b-9a12a011d726["Output\nbam_stats_1"]; 7 --> 96de3c0c-4d7e-423b-8e9b-9a12a011d726; style 96de3c0c-4d7e-423b-8e9b-9a12a011d726 stroke:#2c3143,stroke-width:4px; 8["Filter"]; 6 -->|output| 8; 9["Stats"]; 8 -->|out_file1| 9; 9603a94a-dcd8-4c1f-89cd-bb31d8572783["Output\nbam_stats_2"]; 9 --> 9603a94a-dcd8-4c1f-89cd-bb31d8572783; style 9603a94a-dcd8-4c1f-89cd-bb31d8572783 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 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