workflow-generate-dataset-for-assembly-tutorial

microbiome-metagenomics-assembly/workflow-generate-dataset-for-assembly-tutorial

Author(s)

version Version
1
last_modification Last updated
Jan 15, 2024
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags

Features

Tutorial
hands_on Assembly of metagenomic sequencing data
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00126
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["ℹ️ Input Dataset\nERR2231567_1.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nERR2231567_2.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Cutadapt"];
  0 -->|output| 2;
  1 -->|output| 2;
  3["MEGAHIT"];
  2 -->|out1| 3;
  2 -->|out2| 3;
  4["Bowtie2"];
  2 -->|out1| 4;
  2 -->|out2| 4;
  3 -->|output| 4;
  5["BAM filter"];
  4 -->|output| 5;
  6["BAM filter"];
  4 -->|output| 6;
  7["Convert, Merge, Randomize"];
  5 -->|outfile| 7;
  8["Convert, Merge, Randomize"];
  6 -->|outfile| 8;
  9["Select random lines"];
  7 -->|out_file1| 9;
  10["Select random lines"];
  8 -->|out_file1| 10;
  11["Filter Tabular"];
  9 -->|out_file1| 11;
  12["Filter Tabular"];
  10 -->|out_file1| 12;
  13["Unique"];
  11 -->|output| 13;
  14["Unique"];
  12 -->|output| 14;
  15["Concatenate datasets"];
  13 -->|outfile| 15;
  14 -->|outfile| 15;
  16["seqtk_subseq"];
  2 -->|out1| 16;
  15 -->|out_file1| 16;
  17["seqtk_subseq"];
  2 -->|out2| 17;
  15 -->|out_file1| 17;
  18["FastQC"];
  16 -->|default| 18;
  19["FastQC"];
  17 -->|default| 19;

Inputs

Input Label
Input dataset ERR2231567_1.fastq.gz
Input dataset ERR2231567_2.fastq.gz

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy0 Cutadapt
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0 MEGAHIT
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1 Bowtie2
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 BAM filter
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 BAM filter
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 Convert, Merge, Randomize
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 Convert, Merge, Randomize
random_lines1 Select random lines
random_lines1 Select random lines
toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 Filter Tabular
toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 Filter Tabular
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 Unique
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 Unique
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 Concatenate datasets
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 seqtk_subseq
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 seqtk_subseq
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 FastQC

Tools

Tool Links
random_lines1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/2.5.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.4.5+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/2.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/megahit/megahit/1.2.9+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+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 0e0a2f2cc 2024-01-10 15:47:09 Rename metagenomics topic to microbiome

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/metagenomics-assembly/workflows/workflow-generate-dataset-for-assembly-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