Psilocybin Worflow for Tutorial - Part 1 (upload to fastp)

Open on usegalaxy.eu

flowchart TD
  0["ℹ️ Input Dataset\nSRA_accession_numbers_psilocybin"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nRelabel Identifiers_PsilocybinfromExcel.txt"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Faster Download and Extract Reads in FASTQ"];
  0 -->|output| 2;
  dea91f21-1f15-4724-ba90-63785dc0478a["Output\nraw data"];
  2 --> dea91f21-1f15-4724-ba90-63785dc0478a;
  style dea91f21-1f15-4724-ba90-63785dc0478a stroke:#2c3143,stroke-width:4px;
  3["Flatten collection"];
  2 -->|list_paired| 3;
  4["fastp"];
  2 -->|list_paired| 4;
  06c3acdd-f414-4e4f-9267-bdbf3a5b95eb["Output\ntrimmed data"];
  4 --> 06c3acdd-f414-4e4f-9267-bdbf3a5b95eb;
  style 06c3acdd-f414-4e4f-9267-bdbf3a5b95eb stroke:#2c3143,stroke-width:4px;
  5["Relabel identifiers"];
  1 -->|output| 5;
  3 -->|output| 5;
  6["MultiQC"];
  4 -->|report_json| 6;
  0b7e0763-98c5-40b3-9ab1-1d6105489f5c["Output\nSummary of trimming"];
  6 --> 0b7e0763-98c5-40b3-9ab1-1d6105489f5c;
  style 0b7e0763-98c5-40b3-9ab1-1d6105489f5c stroke:#2c3143,stroke-width:4px;
  7["Falco"];
  4 -->|output_paired_coll| 7;
  8["Falco"];
  5 -->|output| 8;
  9["MultiQC"];
  8 -->|text_file| 9;
  a2eeb1f7-e760-4eb7-9a9a-6c5f4199ac9d["Output\nQC summary of raw data"];
  9 --> a2eeb1f7-e760-4eb7-9a9a-6c5f4199ac9d;
  style a2eeb1f7-e760-4eb7-9a9a-6c5f4199ac9d stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget /training-material/topics/rna-seq/tutorials/upload-qc/workflows/main_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