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