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

variant-analysis-somatic-variant-discovery/somatic-variant-discovery-from-wes-data-using-control-freec

Author(s)
khaled Jumah, Katarzyna Kamieniecka, Wolfgang Maier, Krzysztof Poterlowicz, poterlowicz-lab
version Version
1
last_modification Last updated
Feb 3, 2024
license License
AGPL-3.0-or-later
galaxy-tags Tags
hCNV
variant-analysis
MIRACUM

Features

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

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00267
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
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"];
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  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;
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  75a0f2fc-e9a3-4537-8470-4c1efb5b7be5["Output\nout_chr_sorted_circos"];
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  33 -->|out_chr_sorted_circos| 34;
  33 -->|out_ratio_log2_circos| 34;
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Inputs

Input Label
Input dataset Normal_r1.fastq.gz
Input dataset Normal_r2.fastq.gz
Input dataset Tumor_r1.fastq.gz
Input dataset Tumor_r2.fastq.gz
Input dataset capture_targets_chr5_12_17.bed

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/11.6+galaxy2 Control-FREEC
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9 Circos

Tools

Tool Links
Grep1
__BUILD_LIST__
__EXTRACT_DATASET__
__RELABEL_FROM_FILE__
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/bamleftalign/1.3.6 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_calmd/samtools_calmd/2.0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/circos/circos/0.69.8+galaxy9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/control_freec/control_freec/11.6+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.39+galaxy0 View in ToolShed

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
1 ee30bdca7 2024-01-22 15:03:35 update and fix workflow

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