Make docs deprecated

genepi · Sep 28, 2024 · 05b6daf · 05b6daf
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diff --git a/docs/api.md b/docs/api.md
@@ -1,5 +1,8 @@
 # API Reference
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 The REST APIs provide programmatic ways to submit new jobs and to download data from Michigan Imputation Server. It identifies users using authentication tokens, responses are provided in JSON format.
 
 

diff --git a/docs/contact.md b/docs/contact.md
@@ -1,5 +1,8 @@
 # Contact
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 The complete Michigan Imputation Server source code is available on [GitHub](https://github.com/genepi/imputationserver). Feel free to create issues and pull requests. Before contacting us, please have a look at the [FAQ page](/faq) first. 
 
 Please contact [Christian Fuchsberger](mailto:cfuchsb@umich.edu) in case of other problems.

diff --git a/docs/create-reference-panels.md b/docs/create-reference-panels.md
@@ -1,5 +1,8 @@
 # Create a Reference Panel
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 This tutorial will help you to create your own reference panel and integrate it into Michigan Imputation Server. 
 
 ## Required Software

diff --git a/docs/data-sensitivity.md b/docs/data-sensitivity.md
@@ -1,5 +1,8 @@
 # Data Security
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 Since data is transfered to our server located in Michigan, a wide array of security measures are in force:
 
 - The complete interaction with the server is secured with HTTPS.

diff --git a/docs/docker.md b/docs/docker.md
@@ -1,3 +1,6 @@
 # Michigan Imputation Server on Docker
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 A docker image and instructions are available [here](https://github.com/genepi/imputationserver-docker).
diff --git a/docs/faq.md b/docs/faq.md
@@ -1,5 +1,8 @@
 # Frequently Asked Questions
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 ## I did not receive a password for my imputation job
 Michigan Imputation Server creates a random password for each imputation job. This password is not stored on server-side at any time. If you didn't receive a password, please check your Mail SPAM folder. Please note that we are not able to re-send you the password.  
 

diff --git a/docs/getting-started.md b/docs/getting-started.md
@@ -1,5 +1,8 @@
 # Getting started
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 To use Michigan Imputation Server, a [registration](https://imputationserver.sph.umich.edu/index.html#!pages/register) is required.
 We send an activation mail to the provided address. Please follow the instructions in the email to activate your account. If it doesn't arrive, ensure you have entered the correct email address and check your spam folder.
 

diff --git a/docs/index.md b/docs/index.md
@@ -1,5 +1,7 @@
 # Michigan Imputation Server
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
 
 [Michigan Imputation Server](https://imputationserver.sph.umich.edu) provides a free genotype imputation service using [Minimac4](http://genome.sph.umich.edu/wiki/Minimac4). You can upload phased or unphased GWAS genotypes and receive phased and imputed genomes in return. Our server offers imputation from 1000 Genomes (Phase 1 and 3), CAAPA, [HRC](http://www.haplotype-reference-consortium.org/) and the [TOPMed](http://nhlbiwgs.org/) reference panel. For all uploaded datasets an extensive QC is performed.
 

diff --git a/docs/pgs/faq.md b/docs/pgs/faq.md
@@ -1,5 +1,8 @@
 # Frequently Asked Questions
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 ## Can I use the Polygenic Score Calculation extension without an email address?
 Yes, the extension can also be used with a username without an email. However, without an email, notifications are not sent, and access to genotyped data may be limited.
 

diff --git a/docs/pgs/getting-started.md b/docs/pgs/getting-started.md
@@ -1,5 +1,8 @@
 #  Polygenic Score Calculation
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 We provide an easy to use and user-friendly web interface to apply thousands of published polygenic risk scores to imputed genotypes in an efficient way.
 By extending the popular Michigan Imputation Server the module integrates it seamless into the existing imputation workflow and enables users without knowledge in that field to take advantage of this method.
 The graphical report includes all meta-data about the scores in a single place and helps users to understand and screen thousands of scores in an easy and intuitive way.

diff --git a/docs/pgs/output-files.md b/docs/pgs/output-files.md
@@ -1,5 +1,8 @@
 # Output Files
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 The Polygenic Score Calculation Results CSV file provides Polygenic Score (PGS) values for different samples and associated identifiers. 
 Users can leverage this CSV file to analyze and compare Polygenic Score values across different samples. The data facilitates the investigation of genetic associations and their impact on specific traits or conditions.
 

diff --git a/docs/pgs/pipeline.md b/docs/pgs/pipeline.md
@@ -1,5 +1,8 @@
 # Pipeline
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 ![pipeline.png](images%2Fpipeline.png)
 
 

diff --git a/docs/pgs/reference-panels.md b/docs/pgs/reference-panels.md
@@ -1,5 +1,8 @@
 # Reference Panels for PGS Calculation
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 Our server offers PGS calculation from the following reference panels:
 
 

diff --git a/docs/pgs/report.md b/docs/pgs/report.md
@@ -1,5 +1,8 @@
 # Interactive Report
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 The created report contains a list of all scores, where each score has a different color based on its coverage. The color green indicates that the coverage is very high and nearly all SNPs from the score were also found in the imputed dataset. The color red indicates that very few SNPs were found and the coverage is therefore low.
 
 ![report.png](images/report-01.png)

diff --git a/docs/pgs/scores.md b/docs/pgs/scores.md
@@ -1,5 +1,8 @@
 # Scores
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 We support currently the following PGS repositories out of the box:
 
 ## PGS-Catalog

diff --git a/docs/pgs/tutorial.md b/docs/pgs/tutorial.md
@@ -1,5 +1,7 @@
 # Testing Imputationserver PGS: Step by Step
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
 
 To test Imputationserver PGS, please execute the following steps:
 

diff --git a/docs/pipeline.md b/docs/pipeline.md
@@ -1,5 +1,8 @@
 # Pipeline Overview
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 Our pipeline performs the following steps:
 
 ## Quality Control

diff --git a/docs/prepare-your-data.md b/docs/prepare-your-data.md
@@ -1,5 +1,8 @@
 # Data preparation
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 Michigan Imputation Server accepts VCF files compressed with [bgzip](http://samtools.sourceforge.net/tabix.shtml). Please make sure the following requirements are met:
 
 - Create a separate vcf.gz file for each chromosome.

diff --git a/docs/reference-panels.md b/docs/reference-panels.md
@@ -1,5 +1,8 @@
 # Reference Panels
 
+!!! warning "Deprecated Documentation"
+    ⚠️ This documentation is deprecated and is no longer maintained. The latest documentation can be found at [**Michigan Imputation Server 2**](https://genepi.github.io/michigan-imputationserver/).
+
 Our server offers imputation from the following reference panels: