assembly_with_preprocessing

assembly-assembly-with-preprocessing/assembly-with-preprocessing

Author(s)

version Version
1
last_modification Last updated
Apr 22, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
GTN
assembly

Features

Tutorial
hands_on Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
workflow Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00002
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 Collection\nCollection of paired short-reads data"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nCollection of long-reads data"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Samtools fastx"];
  7 -->|outputsam| 10;
  11["Samtools fastx"];
  9 -->|outputsam| 11;
  12["Collapse Collection"];
  10 -->|nonspecific| 12;
  13["Zip Collection"];
  11 -->|forward| 13;
  11 -->|reverse| 13;
  14["Collapse Collection"];
  11 -->|forward| 14;
  15["Collapse Collection"];
  11 -->|reverse| 15;
  16["seqtk_sample"];
  14 -->|output| 16;
  17["seqtk_sample"];
  15 -->|output| 17;
  18["Create assemblies with Unicycler"];
  12 -->|output| 18;
  16 -->|default| 18;
  17 -->|default| 18;
  19["Bandage Info"];
  18 -->|assembly_graph| 19;
  2["fastp: Trimmed Illumina Reads"];
  0 -->|output| 2;
  20["Filter sequences by length"];
  18 -->|assembly| 20;
  21["Bandage Image"];
  18 -->|assembly_graph| 21;
  3["NanoPlot"];
  1 -->|output| 3;
  4["Map with minimap2"];
  1 -->|output| 4;
  5["MultiQC"];
  2 -->|report_json| 5;
  6["Bowtie2"];
  2 -->|output_paired_coll| 6;
  7["Samtools view"];
  4 -->|alignment_output| 7;
  8["Samtools stats"];
  4 -->|alignment_output| 8;
  9["Samtools view"];
  6 -->|output| 9;

Inputs

Input Label
Input dataset collection Collection of paired short-reads data
Input dataset collection Collection of long-reads data

Outputs

From Output Label
Input dataset collection Collection of paired short-reads data
Input dataset collection Collection of long-reads data
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 Samtools fastx
__ZIP_COLLECTION__ Zip Collection
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2 seqtk_sample
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2 seqtk_sample
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 Create assemblies with Unicycler
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 Bandage Info
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 fastp fastp: Trimmed Illumina Reads
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2 Filter sequences by length
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 Bandage Image
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 NanoPlot
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1 Map with minimap2
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 MultiQC
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 Bowtie2
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 Samtools stats

Tools

Tool Links
__ZIP_COLLECTION__
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_image/0.8.1+galaxy2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/bandage/bandage_info/0.8.1+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.17+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/nanoplot/nanoplot/1.25.0+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/samtools_fastx/samtools_fastx/1.9+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.9+galaxy1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_sample/1.3.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.8.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 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
2 fc35e6581 2020-04-22 12:33:13 add annotations
1 7ed054469 2020-04-22 11:34:36 readd workflows

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/assembly/tutorials/assembly-with-preprocessing/workflows/assembly_with_preprocessing.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