NGS_tutorial
introduction-galaxy-intro-ngs-data-managment/ngs-intro-workflow
Launch in Tutorial Mode
question
galaxy-download Download
galaxy-download Download
flowchart TD 0["ℹ️ Input Dataset\nAccessions"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nGenome"]; style 1 stroke:#2c3143,stroke-width:4px; 2["Faster Download and Extract Reads in FASTQ"]; 0 -->|output| 2; 3["fastp"]; 2 -->|list_paired| 3; 4["Map with BWA-MEM"]; 3 -->|output_paired_coll| 4; 1 -->|output| 4; 5["Samtools view"]; 4 -->|bam_output| 5; 6["MarkDuplicates"]; 5 -->|outputsam| 6; 7["Samtools stats"]; 6 -->|outFile| 7; 8["Realign reads"]; 6 -->|outFile| 8; 1 -->|output| 8; 9["MultiQC"]; 3 -->|report_json| 9; 6 -->|metrics_file| 9; 7 -->|output| 9; 10["Insert indel qualities"]; 8 -->|realigned| 10; 1 -->|output| 10; 11["Call variants"]; 10 -->|output| 11; 1 -->|output| 11; 12["SnpEff eff:"]; 11 -->|variants| 12; 13["SnpSift Extract Fields"]; 12 -->|snpeff_output| 13; 14["Collapse Collection"]; 13 -->|output| 14;
Inputs
Input | Label |
---|---|
Accessions | Accessions |
Genome | Genome |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump/2.10.8+galaxy0 | Faster Download and Extract Reads in FASTQ | |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 | fastp | |
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1 | Map with BWA-MEM | |
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy2 | Samtools view | |
toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2 | MarkDuplicates | |
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 | Samtools stats | |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_viterbi/lofreq_viterbi/2.1.5+galaxy0 | Realign reads | |
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1 | MultiQC | |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_indelqual/lofreq_indelqual/2.1.5+galaxy0 | Insert indel qualities | |
toolshed.g2.bx.psu.edu/repos/iuc/lofreq_call/lofreq_call/2.1.5+galaxy1 | Call variants | |
toolshed.g2.bx.psu.edu/repos/iuc/snpeff_sars_cov_2/snpeff_sars_cov_2/4.5covid19 | SnpEff eff: | |
toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_extractFields/4.3+t.galaxy0 | SnpSift Extract Fields | |
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 | Collapse Collection |
Tools
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-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
Version History
Version | Commit | Time | Comments |
---|---|---|---|
2 | ca2265825 | 2021-02-11 19:01:41 | workflow changes |
1 | 211e2c843 | 2021-02-11 18:51:43 | Updated NGS tutorial for GTN Smörgåsbord |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/ngs_intro_workflow.ga -O workflow.ga workflow-to-tools -w workflow.ga -o tools.yaml shed-tools install -g GALAXY -a API_KEY -t tools.yaml workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows