NGS_tutorial

Run Workflow in Galaxy

• Galaxy Australia
• Galaxy Europe
• Galaxy France
• Galaxy Main
• Import to another server (≥23.0+ only!)

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["Download sequencing data"];
  0 -->|output| 2;
  ceeab6ee-59e9-4ea1-8301-29e9763da7e7["Output\nLog file"];
  2 --> ceeab6ee-59e9-4ea1-8301-29e9763da7e7;
  style ceeab6ee-59e9-4ea1-8301-29e9763da7e7 stroke:#2c3143,stroke-width:4px;
  dc27aec8-9751-4877-a761-3e0df6196120["Output\nUnpaired datasets"];
  2 --> dc27aec8-9751-4877-a761-3e0df6196120;
  style dc27aec8-9751-4877-a761-3e0df6196120 stroke:#2c3143,stroke-width:4px;
  c5eb96e5-d151-4c56-9d49-6d38967846ef["Output\nPaired-end datasets"];
  2 --> c5eb96e5-d151-4c56-9d49-6d38967846ef;
  style c5eb96e5-d151-4c56-9d49-6d38967846ef stroke:#2c3143,stroke-width:4px;
  8e89df59-0358-4ed8-9e73-4874fa63da74["Output\nSingle-end datasets"];
  2 --> 8e89df59-0358-4ed8-9e73-4874fa63da74;
  style 8e89df59-0358-4ed8-9e73-4874fa63da74 stroke:#2c3143,stroke-width:4px;
  3["Adapter trimming with fastp"];
  2 -->|list_paired| 3;
  6134ed21-60d2-4463-94ed-90d405fa79c7["Output\nPaired-end Collection"];
  3 --> 6134ed21-60d2-4463-94ed-90d405fa79c7;
  style 6134ed21-60d2-4463-94ed-90d405fa79c7 stroke:#2c3143,stroke-width:4px;
  23007acc-0e39-4c79-a501-f7bfdbe4eca4["Output\nReport in HTML format"];
  3 --> 23007acc-0e39-4c79-a501-f7bfdbe4eca4;
  style 23007acc-0e39-4c79-a501-f7bfdbe4eca4 stroke:#2c3143,stroke-width:4px;
  c0ae08ab-5964-4e24-91ea-2b56592450fd["Output\nReport in JSON format"];
  3 --> c0ae08ab-5964-4e24-91ea-2b56592450fd;
  style c0ae08ab-5964-4e24-91ea-2b56592450fd stroke:#2c3143,stroke-width:4px;
  4["Map sequencing reads to reference genome with BWA-MEM"];
  3 -->|output_paired_coll| 4;
  1 -->|output| 4;
  c5884bbf-7972-402e-9679-bf112e435c5d["Output\nMapping BAM output"];
  4 --> c5884bbf-7972-402e-9679-bf112e435c5d;
  style c5884bbf-7972-402e-9679-bf112e435c5d stroke:#2c3143,stroke-width:4px;
  5["Samtools view"];
  4 -->|bam_output| 5;
  4cd8f23c-ee1e-4587-b880-a016bfda9b9a["Output\nMapping SAM output"];
  5 --> 4cd8f23c-ee1e-4587-b880-a016bfda9b9a;
  style 4cd8f23c-ee1e-4587-b880-a016bfda9b9a stroke:#2c3143,stroke-width:4px;
  6["Removing duplicate sequences originating from library preparation artifacts and sequencing artifacts with MarkDuplicates"];
  5 -->|outputsam| 6;
  8e8357a3-d8e6-4a28-a000-9897240a6c7f["Output\nMarkDuplicates BAM"];
  6 --> 8e8357a3-d8e6-4a28-a000-9897240a6c7f;
  style 8e8357a3-d8e6-4a28-a000-9897240a6c7f stroke:#2c3143,stroke-width:4px;
  1d2eaa9f-336a-4954-82b0-526da01d43eb["Output\nMarkDuplicates Metrics"];
  6 --> 1d2eaa9f-336a-4954-82b0-526da01d43eb;
  style 1d2eaa9f-336a-4954-82b0-526da01d43eb stroke:#2c3143,stroke-width:4px;
  7["Correcting the misalignments around insertions and deletions with Realign reads"];
  6 -->|outFile| 7;
  1 -->|output| 7;
  af463107-789c-49cf-8dfa-37799b4bea9b["Output\nRealigned reads BAM file"];
  7 --> af463107-789c-49cf-8dfa-37799b4bea9b;
  style af463107-789c-49cf-8dfa-37799b4bea9b stroke:#2c3143,stroke-width:4px;
  8["Samtools stats"];
  6 -->|outFile| 8;
  c4dc38a6-eb6b-4a52-b38b-a88a73682928["Output\nStatistics for BAM dataset"];
  8 --> c4dc38a6-eb6b-4a52-b38b-a88a73682928;
  style c4dc38a6-eb6b-4a52-b38b-a88a73682928 stroke:#2c3143,stroke-width:4px;
  9["Adding the indel qualities into our alignment file via Insert indel qualities"];
  7 -->|realigned| 9;
  1 -->|output| 9;
  6dee7ec9-9a2e-48a6-9172-fe5a1bb9f9b0["Output\nRealigned BAM dataset with indel qualities"];
  9 --> 6dee7ec9-9a2e-48a6-9172-fe5a1bb9f9b0;
  style 6dee7ec9-9a2e-48a6-9172-fe5a1bb9f9b0 stroke:#2c3143,stroke-width:4px;
  10["Summarizing the analyses with MultiQC"];
  3 -->|report_json| 10;
  6 -->|metrics_file| 10;
  8 -->|output| 10;
  8c8064a6-11fe-4d20-afa0-39dc8fbaa2b0["Output\nMultiQC Stat table"];
  10 --> 8c8064a6-11fe-4d20-afa0-39dc8fbaa2b0;
  style 8c8064a6-11fe-4d20-afa0-39dc8fbaa2b0 stroke:#2c3143,stroke-width:4px;
  d83d789f-6723-4360-ac69-47a20db5dd15["Output\nMultiQC HTML report"];
  10 --> d83d789f-6723-4360-ac69-47a20db5dd15;
  style d83d789f-6723-4360-ac69-47a20db5dd15 stroke:#2c3143,stroke-width:4px;
  11["Calling the Variants using lofreq Call variants"];
  9 -->|output| 11;
  1 -->|output| 11;
  e6369b39-d95c-4c11-870d-855f833aa2bd["Output\nAll called variants"];
  11 --> e6369b39-d95c-4c11-870d-855f833aa2bd;
  style e6369b39-d95c-4c11-870d-855f833aa2bd stroke:#2c3143,stroke-width:4px;
  12["Annotating the variant effects with SnpEff eff"];
  11 -->|variants| 12;
  bbec359e-3ccb-4173-9fc3-6eff1edb0864["Output\nHTML summary of results "];
  12 --> bbec359e-3ccb-4173-9fc3-6eff1edb0864;
  style bbec359e-3ccb-4173-9fc3-6eff1edb0864 stroke:#2c3143,stroke-width:4px;
  1bab9bf4-8788-4c7a-b12a-11afceb90a54["Output\nVariant dataset with added variant effects"];
  12 --> 1bab9bf4-8788-4c7a-b12a-11afceb90a54;
  style 1bab9bf4-8788-4c7a-b12a-11afceb90a54 stroke:#2c3143,stroke-width:4px;
  13["Creating table of variants using SnpSift Extract Fields"];
  12 -->|snpeff_output| 13;
  4bfe24cc-6e25-47ad-afd1-13b1729fea01["Output\nVariant dataset with added variant effects in tabular format"];
  13 --> 4bfe24cc-6e25-47ad-afd1-13b1729fea01;
  style 4bfe24cc-6e25-47ad-afd1-13b1729fea01 stroke:#2c3143,stroke-width:4px;
  14["Collapsing the data into a single dataset"];
  13 -->|output| 14;
  dda400de-8467-4861-8cf1-78594dce83a3["Output\nSummarized variant analysis result dataset"];
  14 --> dda400de-8467-4861-8cf1-78594dce83a3;
  style dda400de-8467-4861-8cf1-78594dce83a3 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-ngs-data-managment/workflows/NGS_tutorial.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