Essential genes detection with Transposon insertion sequencing

genome-annotation-tnseq/essential-genes-detection-transposon-insertion-sequencing-workflow

Author(s)

version Version
1
last_modification Last updated
Oct 18, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
genome-annotation

Features

Tutorial
hands_on Essential genes detection with Transposon insertion sequencing

Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00100
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\nTnseq-Tutorial-reads.fastqsanger.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncondition_barcodes.fasta"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nconstruct_barcodes.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nstaph_aur.fasta"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nstaph_aur.gff3"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Cutadapt"];
  0 -->|output| 5;
  1 -->|output| 5;
  6["Nucleotide subsequence search"];
  3 -->|output| 6;
  7["Convert GFF3"];
  4 -->|output| 7;
  8["Cutadapt"];
  5 -->|split_output| 8;
  9["Cut"];
  6 -->|output| 9;
  10["Cut"];
  6 -->|output| 10;
  11["Cutadapt"];
  8 -->|out1| 11;
  12["Compute"];
  10 -->|out_file1| 12;
  13["Cutadapt"];
  11 -->|out1| 13;
  2 -->|output| 13;
  14["Cut"];
  12 -->|out_file1| 14;
  15["Cutadapt"];
  13 -->|split_output| 15;
  16["Map with Bowtie for Illumina"];
  3 -->|output| 16;
  15 -->|out1| 16;
  17["bamCoverage"];
  16 -->|output| 17;
  18["Join"];
  17 -->|outFileName| 18;
  9 -->|out_file1| 18;
  19["Join"];
  17 -->|outFileName| 19;
  14 -->|out_file1| 19;
  20["Cut"];
  18 -->|output| 20;
  21["Cut"];
  19 -->|output| 21;
  22["Sort"];
  20 -->|out_file1| 22;
  23["Compute"];
  21 -->|out_file1| 23;
  24["Cut"];
  23 -->|out_file1| 24;
  25["Sort"];
  24 -->|out_file1| 25;
  26["Join"];
  22 -->|outfile| 26;
  25 -->|outfile| 26;
  27["Compute"];
  26 -->|output| 27;
  28["Cut"];
  27 -->|out_file1| 28;
  29["Sort"];
  28 -->|out_file1| 29;
  30["Gumbel"];
  7 -->|output| 30;
  29 -->|outfile| 30;
  31["Filter"];
  30 -->|sites| 31;
  32["Extract Dataset"];
  31 -->|out_file1| 32;
  8796f62f-4676-4ad2-b085-7597f894c32c["Output\ncontrol"];
  32 --> 8796f62f-4676-4ad2-b085-7597f894c32c;
  style 8796f62f-4676-4ad2-b085-7597f894c32c stroke:#2c3143,stroke-width:4px;
  33["Extract Dataset"];
  31 -->|out_file1| 33;
  bd014de4-708e-419c-bd1e-8bf350661aad["Output\ncondition"];
  33 --> bd014de4-708e-419c-bd1e-8bf350661aad;
  style bd014de4-708e-419c-bd1e-8bf350661aad stroke:#2c3143,stroke-width:4px;
  34["Join"];
  32 -->|output| 34;
  33 -->|output| 34;
  5cdfb5c9-c677-41dc-a838-c4a61d62f5be["Output\nessential_both"];
  34 --> 5cdfb5c9-c677-41dc-a838-c4a61d62f5be;
  style 5cdfb5c9-c677-41dc-a838-c4a61d62f5be stroke:#2c3143,stroke-width:4px;
  35["Join"];
  32 -->|output| 35;
  33 -->|output| 35;
  8b2b65ea-37c3-43d2-b416-38f8f920fbd9["Output\nessential_control"];
  35 --> 8b2b65ea-37c3-43d2-b416-38f8f920fbd9;
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  36["Join"];
  32 -->|output| 36;
  33 -->|output| 36;
  37639319-b053-4fbc-bf61-fd3e38263502["Output\nessential_condition"];
  36 --> 37639319-b053-4fbc-bf61-fd3e38263502;
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Inputs

Input Label
Tnseq-Tutorial-reads.fastqsanger.gz Tnseq-Tutorial-reads.fastqsanger.gz
condition_barcodes.fasta condition_barcodes.fasta
construct_barcodes.fasta construct_barcodes.fasta
staph_aur.fasta staph_aur.fasta
staph_aur.gff3 staph_aur.gff3

Outputs

From Output Label
Tnseq-Tutorial-reads.fastqsanger.gz Tnseq-Tutorial-reads.fastqsanger.gz
condition_barcodes.fasta condition_barcodes.fasta
construct_barcodes.fasta construct_barcodes.fasta
staph_aur.fasta staph_aur.fasta
staph_aur.gff3 staph_aur.gff3
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 Cutadapt
toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2 Nucleotide subsequence search
toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0 Convert GFF3
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 Cutadapt
Cut1 Cut
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 Cutadapt
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 Compute
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 Cutadapt
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 Cutadapt
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0 Map with Bowtie for Illumina
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 bamCoverage
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 Join
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 Join
Cut1 Cut
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 Sort
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 Compute
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 Sort
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 Join
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 Compute
Cut1 Cut
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 Sort
toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0 Gumbel
Filter1 Filter
__EXTRACT_DATASET__ Extract Dataset
__EXTRACT_DATASET__ Extract Dataset
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 Join
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 Join
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 Join

Tools

Tool Links
Cut1
Filter1
__EXTRACT_DATASET__
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/find_subsequences/bg_find_subsequences/0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool/1.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/1.3.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/gff_to_prot/gff_to_prot/3.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/transit_gumbel/transit_gumbel/3.0.2+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 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
3 bc41adb9e 2020-10-18 20:22:36 Rename workflow.
2 50c52377e 2020-10-18 19:12:52 Update workflow test.
1 708ae9c5d 2020-10-18 10:40:59 Updated workflow and test.

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.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