QC + Mapping + Counting - Ref Based RNA Seq - Transcriptomics - GTN - subworkflows
transcriptomics-ref-based/qc-mapping-counting
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Inputs
Input | Label |
---|---|
Input dataset collection | Paired list collection with PE fastqs |
Input dataset | Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz |
Outputs
From | Output | Label |
---|---|---|
FastQC | ||
cutadapt | ||
STAR + multiQC | ||
more QC | ||
Determine strandness | ||
count STAR | ||
count featureCount |
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 |
---|---|---|---|
19 | a1251f286 | 2024-07-05 09:38:54 | Removed 'comments' tags |
18 | 068c0f303 | 2024-07-05 09:28:05 | Updated 'QC + Mapping + Counting' workflow |
17 | 3377d5c6f | 2023-10-20 13:31:21 | update workflow to have steps in the same order as in the tutorial |
16 | 41dead43e | 2023-05-02 10:31:07 | add mo orcid to workflows |
15 | 36eb5cf82 | 2023-04-28 17:26:00 | update workflows and tests |
14 | f35bb9e74 | 2023-04-27 13:30:02 | update zenodo try to make workflow test working |
13 | 8fc9c9026 | 2023-04-25 07:46:15 | add creators and licence to workflows |
12 | dc21d9ddb | 2023-04-22 08:29:08 | update images and results, rearrange workflow for part1 |
11 | 9921a8623 | 2023-04-21 12:37:10 | Update first part of the tutorial |
10 | 6203157c4 | 2022-05-05 08:25:29 | revert bdc1fd3 |
9 | 4d2f611a6 | 2022-04-28 15:20:51 | subset BAM before gene body coverage |
8 | bdc1fd3ce | 2022-04-28 08:35:56 | switch order of fastqc and flatten |
7 | 8ff9bda0f | 2022-04-14 21:15:02 | update workflow to fit test |
6 | bae8287b9 | 2022-04-14 12:52:02 | update qc workflow and test |
5 | e08c38b2b | 2022-04-05 19:36:51 | add tag |
4 | 35d565217 | 2022-04-05 13:18:22 | update workflows |
3 | 667ff3de9 | 2020-01-22 10:59:29 | annotation |
2 | eb4d724e0 | 2020-01-15 10:41:35 | Workflow renaming |
1 | e477f2b7f | 2019-09-10 09:22:59 | Split workflow and add more tests |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/ref-based/workflows/qc-mapping-counting.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