Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nNormal_r1.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nNormal_r2.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nTumor_r1.fastq.gz"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Create text file"];
  4["ℹ️ Input Dataset\nTumor_r2.fastq.gz"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\ncapture_targets_chr5_12_17.bed"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["FastQC"];
  0 -->|output| 6;
  7["Trimmomatic"];
  0 -->|output| 7;
  1 -->|output| 7;
  8["FastQC"];
  1 -->|output| 8;
  9["FastQC"];
  2 -->|output| 9;
  10["Trimmomatic"];
  2 -->|output| 10;
  4 -->|output| 10;
  11["FastQC"];
  4 -->|output| 11;
  12["FastQC"];
  7 -->|fastq_out_r2_paired| 12;
  13["Map with BWA-MEM"];
  7 -->|fastq_out_r1_paired| 13;
  7 -->|fastq_out_r2_paired| 13;
  14["FastQC"];
  7 -->|fastq_out_r1_paired| 14;
  15["FastQC"];
  10 -->|fastq_out_r2_paired| 15;
  16["Map with BWA-MEM"];
  10 -->|fastq_out_r1_paired| 16;
  10 -->|fastq_out_r2_paired| 16;
  17["FastQC"];
  10 -->|fastq_out_r1_paired| 17;
  18["MultiQC"];
  9 -->|text_file| 18;
  6 -->|text_file| 18;
  8 -->|text_file| 18;
  11 -->|text_file| 18;
  19["Build list"];
  13 -->|bam_output| 19;
  16 -->|bam_output| 19;
  20["MultiQC"];
  12 -->|text_file| 20;
  14 -->|text_file| 20;
  15 -->|text_file| 20;
  17 -->|text_file| 20;
  21["Relabel identifiers"];
  3 -->|outfile| 21;
  19 -->|output| 21;
  22["Samtools view"];
  21 -->|output| 22;
  23["RmDup"];
  22 -->|outputsam| 23;
  24["BamLeftAlign"];
  23 -->|output1| 24;
  25["Samtools calmd"];
  24 -->|output_bam| 25;
  26["Samtools view"];
  25 -->|calmd_output| 26;
  27["Samtools view"];
  25 -->|calmd_output| 27;
  28["Select"];
  26 -->|outputsam| 28;
  29["Replace Text"];
  28 -->|out_file1| 29;
  30["Samtools view"];
  27 -->|outputsam| 30;
  29 -->|outfile| 30;
  31["Extract Tumor read"];
  30 -->|outputsam| 31;
  32["Extract normal read"];
  30 -->|outputsam| 32;
  33["Control-FREEC"];
  5 -->|output| 33;
  32 -->|output| 33;
  31 -->|output| 33;
  2f4f45dd-d145-4078-aed9-5d832c51923b["Output\nout_sample_info"];
  33 --> 2f4f45dd-d145-4078-aed9-5d832c51923b;
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  13edcdd6-d7f6-4e0f-976e-1032084accf1["Output\nout_sample_coord"];
  33 --> 13edcdd6-d7f6-4e0f-976e-1032084accf1;
  style 13edcdd6-d7f6-4e0f-976e-1032084accf1 stroke:#2c3143,stroke-width:4px;
  ac78da9a-8aa8-45ce-a2d1-3c366783fa60["Output\nout_control_raw"];
  33 --> ac78da9a-8aa8-45ce-a2d1-3c366783fa60;
  style ac78da9a-8aa8-45ce-a2d1-3c366783fa60 stroke:#2c3143,stroke-width:4px;
  213ea0be-1ec6-469b-9556-69682bba69fe["Output\nout_sample_raw"];
  33 --> 213ea0be-1ec6-469b-9556-69682bba69fe;
  style 213ea0be-1ec6-469b-9556-69682bba69fe stroke:#2c3143,stroke-width:4px;
  59a99e4f-01ef-4118-8777-63707e8b1696["Output\nout_ratio_log2_circos"];
  33 --> 59a99e4f-01ef-4118-8777-63707e8b1696;
  style 59a99e4f-01ef-4118-8777-63707e8b1696 stroke:#2c3143,stroke-width:4px;
  75a0f2fc-e9a3-4537-8470-4c1efb5b7be5["Output\nout_chr_sorted_circos"];
  33 --> 75a0f2fc-e9a3-4537-8470-4c1efb5b7be5;
  style 75a0f2fc-e9a3-4537-8470-4c1efb5b7be5 stroke:#2c3143,stroke-width:4px;
  662d214b-3d22-4f67-a4ef-a77b106d1535["Output\nout_gc_profile"];
  33 --> 662d214b-3d22-4f67-a4ef-a77b106d1535;
  style 662d214b-3d22-4f67-a4ef-a77b106d1535 stroke:#2c3143,stroke-width:4px;
  02c14e20-cccd-4804-bbb6-13323afeda2e["Output\nout_mg_log2_png"];
  33 --> 02c14e20-cccd-4804-bbb6-13323afeda2e;
  style 02c14e20-cccd-4804-bbb6-13323afeda2e stroke:#2c3143,stroke-width:4px;
  189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7["Output\nout_mg_png"];
  33 --> 189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7;
  style 189dc4ef-a15f-49cc-9c6e-dff3dbd27ad7 stroke:#2c3143,stroke-width:4px;
  14aba5a4-1ade-477e-b937-7714038f3fd3["Output\nout_sample_subclones"];
  33 --> 14aba5a4-1ade-477e-b937-7714038f3fd3;
  style 14aba5a4-1ade-477e-b937-7714038f3fd3 stroke:#2c3143,stroke-width:4px;
  61323e5f-7846-47e9-a0b3-d79f64ca2bd8["Output\nout_sample_ratio"];
  33 --> 61323e5f-7846-47e9-a0b3-d79f64ca2bd8;
  style 61323e5f-7846-47e9-a0b3-d79f64ca2bd8 stroke:#2c3143,stroke-width:4px;
  34["Circos"];
  33 -->|out_chr_sorted_circos| 34;
  33 -->|out_ratio_log2_circos| 34;
  23ea7d87-b936-4879-bfaa-beb1e141834e["Output\noutput_png"];
  34 --> 23ea7d87-b936-4879-bfaa-beb1e141834e;
  style 23ea7d87-b936-4879-bfaa-beb1e141834e stroke:#2c3143,stroke-width:4px;

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

• 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variant-discovery/workflows/Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC.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