Update Session 2 and remove old workshops

docs/workshops/ASHG2023/Session2.md

@@ -9,7 +9,7 @@ Welcome to Session 2! In this session you will learn how to submit a job on Mich
 ## Getting Started
 As a quick start, the following video includes all required steps to submit and monitor a job using the graphical web interface.
 
-<iframe width="560" height="315" src="https://www.youtube.com/embed/BLTPHWuMF0Q" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+<iframe width="560" height="315" src="https://www.youtube.com/embed/HMP76DpL_I0?si=GSFsFMbqJQFVUhJj" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
 
 
 ## Run a job on your own
@@ -23,17 +23,18 @@ The UI includes several parameters which need to be specified. Our [Getting Star
 
 We are providing two data datasets that can be downloaded from below. In case the unphased dataset is selected, an additional phasing step using Eagle is automatically performed. For this demo, we recommend selecting the **HapMap 2 panel** (Input parameter 'Reference panel') to get your results as quick as possible. Please also have a look at our [supported reference panels](https://imputationserver.readthedocs.io/en/latest/reference-panels/) when using MIS in a production setup.
 
-!!! tip
- You can also copy/paste the URL from below and change "File Upload" to "URLs (HTTP)" load the data from a remote server (GitHub in this case).
-
-- [Phased dataset chr20 hg19](https://github.com/genepi/imputationserver-ashg22/raw/master/files/chr20.R50.merged.1.330k.recode.small.vcf.gz)
-- [Unphased dataset chr20 hg19](https://github.com/genepi/imputationserver-ashg22/raw/master/files/chr20.R50.merged.1.330k.recode.unphased.small.vcf.gz)
+- [Phased dataset chr20 hg19](https://github.com/genepi/imputationserver-ashg/raw/main/files/chr20.R50.merged.1.330k.recode.small.vcf.gz)
+- [Unphased dataset chr20 hg19](https://github.com/genepi/imputationserver-ashg/raw/main/files/chr20.R50.merged.1.330k.recode.unphased.small.vcf.gz)
 
 ## Submission Page - Submit
 After all parameters have been selected and you click 'submit', the job will be added to our Input Validation and QC queue. Please have a look at our [Data Preparation Guide](https://imputationserver.readthedocs.io/en/latest/prepare-your-data) to learn how to prepare your dataset using a pre-imputation tool.
 
 ## Monitor Jobs, Download Data
 If the job passes the QC step, it will be added to our long-time queue. As soon as your job is finished, you will receive an email with the password to download and encrypt your data. Also checkout our [Pipeline Overview Guide](https://imputationserver.readthedocs.io/en/latest/pipeline/) to learn more about the different internal parameters. The complete source code can also be found on [GitHub](https://imputationserver.sph.umich.edu).
 
+## QC Results 
+A simple QC report including the frequency plot is available [here](https://htmlpreview.github.io/?https://github.com/genepi/imputationserver-ashg/blob/main/files/qcreport.html).
+
+
 # Contact
 If you have any questions please write [me an email](mailto:sebastian.schoenherr@i-med.ac.at) or contact me on [Twitter](https://twitter.com/seppinho).

mkdocs.yml

@@ -21,23 +21,6 @@ nav:
  - "Session 4: Imputation Bot and PGS Server": workshops/ASHG2023/Session4.md
  - "Session 5: HLA Imputation": workshops/ASHG2023/Session5.md
  - "Session 6: TOPMed Imputation Server": workshops/ASHG2023/Session6.md
-- ASHG2022:
- - Overview: workshops/ASHG2022.md
- - "Session 1: Imputation and the Server": workshops/ASHG2022/Session1.md
- - "Session 2: Run a job, Data Preparation and Data Download": workshops/ASHG2022/Session2.md
- - "Session 3: Performing GWAS using imputed data": workshops/ASHG2022/Session3.md
- - "Session 4: Imputation Bot and PGS Server": workshops/ASHG2022/Session4.md
- - "Session 5: HLA Imputation": workshops/ASHG2022/Session5.md
- - "Session 6: TOPMed Imputation Server": workshops/ASHG2022/Session6.md
-- ASHG2020:
- - Overview: workshops/ASHG2020.md
- - "Session 1: Imputation and the Server": workshops/ASHG2020/Session1.md
- - "Session 2: Run a job, Quality Control and Data Preparation": workshops/ASHG2020/Session2.md
- - "Session 3: Tracking runs and downloading data": workshops/ASHG2020/Session3.md
- - "Session 4: Performing GWAS using imputed data": workshops/ASHG2020/Session4.md
- - "Session 5: Imputation bot": workshops/ASHG2020/Session5.md
- - "Session 6: TOPMed Imputation Server": workshops/ASHG2020/Session6.md
- - "Session 7: Imputation panels": workshops/ASHG2020/Session7.md
 - Contact: contact.md