Merge branch 'master' of https://github.com/genepi/imputationserver i…

…nto release

# Conflicts:
#	docs/api.md

docs/api.md

@@ -12,80 +12,34 @@ _**Note:** the tokens from Michigan Imputation Server and TOPMed Imputation Serv
 ## Job Submission
 The API allows setting several imputation parameters.
 
-### Michigan Imputation Server Job Submission
-
-URL: https://imputationserver.sph.umich.edu/api/v2
-POST /jobs/submit/minimac4
-
-The following parameters can be set:
-
-| Parameter        | Values           | Default Value  |  Required  |
-| ------------- |:-------------| :-----|---|
-| files         | /path/to/file |  | **x** |
-| mode          | `qconly`<br> `phasing` <br> `imputation`     | `imputation`   | |
-| password      | user-defined password      |  auto generated and send by mail  | |
-| files-source  | `file-upload`<br> `sftp`<br> `http`     |  `file-upload`  | |
-| refpanel      | `apps@hapmap-2`<br> `apps@hrc-r1.1`<br> `apps@1000g-phase-1`<br> `apps@1000g-phase-3-v5` <br> `apps@genome-asia-panel@1.0.0` <br> `apps@cappa` | - | **x** |
-| phasing     | `eagle`<br> `no_phasing`      |  `eagle`  | |
-| population  | `eur`<br> `afr`<br> `asn`<br> `amr`<br> `sas`<br> `eas`<br> `AA`<br> `mixed`      |  -  | **x** |
-| build       | `hg19`<br> `hg38` | `hg19`  | |
-| r2Filter    | `0` <br> `0.001` <br> `0.1` <br> `0.2` <br> `0.3` | `0`  | |
-
 ### TOPMed Imputation Server Job Submission
 
 URL: https://imputation.biodatacatalyst.nhlbi.nih.gov/api/v2
-POST /jobs/submit/imputationserver@1.2.7
+POST /jobs/submit/imputationserver@1.7.3
 
 The following parameters can be set:
 
-| Parameter        | Values           | Default Value  |
-| ------------- |:-------------| :-----|
-| input-files      | /path/to/file |  |
-| input-mode | qconly, imputation     | imputation   |
-| input-password | user-defined password      |  auto  |
-| input-files-source | file-upload, sftp, http     |  default: file-upload  |
-| input-refpanel     | apps@topmed-r2@1.0.0     | - |
-| input-phasing | eagle      |  eagle  |
-| input-population | all, mixed      |  all  |
+| Parameter      | Values                                            | Default Value  |  Required  |
+| ----------- |:--------------------------------------------------| :-----|---|
+| job-name    | (user specified)                                  |  |  |
+| files       | /path/to/file                                     |  | **x** |
+| mode        | `qconly`<br> `phasing` <br> `imputation`          | `imputation`   | |
+| refpanel    | `apps@topmed-r2@1.0.0`                            | - | **x** |
+| phasing     | `eagle`<br> `no_phasing`                          |  `eagle`  | |
+| build       | `hg19`<br> `hg38`                                 | `hg19`  | |
+| r2Filter    | `0` <br> `0.001` <br> `0.1` <br> `0.2` <br> `0.3` | `0`  | |
 
 
 ### Examples
 
 ### Examples: curl
 
-#### Submit a single file
-
-To submit a job please change `/path-to/file.vcf.gz` to a valid vcf file and update `TOKEN` with your API Token:
-
-
-Command:
-
-```sh
-TOKEN="YOUR-API-TOKEN";
-
-curl https://imputationserver.sph.umich.edu/api/v2/jobs/submit/minimac4 \
-  -H "X-Auth-Token: $TOKEN" \
-  -F "files=@/path-to/file.vcf.gz" \
-  -F "refpanel=apps@1000g-phase-3-v5" \
-  -F "population=eur"
-```
-
-Response:
-
-```json
-{
-  "id":"job-20160504-161420",
-  "message":"Your job was successfully added to the job queue.",
-  "success":true
-}
-```
-
 #### Submit a single file using TOPMed 
 
 To submit a job please change `/path-to-file` to the actual path.
 
 ```sh
-curl -H "X-Auth-Token: <your-API-token>" -F "input-files=@/path-to-file" -F "input-refpanel=apps@topmed-r2@1.0.0" -F "input-phasing=eagle" https://imputation.biodatacatalyst.nhlbi.nih.gov/api/v2/jobs/submit/imputationserver@1.2.7
+curl -H "X-Auth-Token: <your-API-token>" -F "input-files=@/path-to-file" -F "input-refpanel=apps@topmed-r2@1.0.0" -F "input-phasing=eagle" https://imputation.biodatacatalyst.nhlbi.nih.gov/api/v2/jobs/submit/imputationserver@1.7.3
 ```
 
 #### Submit multiple files using 1000 Genomes Phase 3

docs/getting-started.md

@@ -41,12 +41,7 @@ The Michigan Imputation Server has several additional reference panels available
 
 More details about all available reference panels can be found [here](/reference-panels/).
 
-### Input files
-
-VCF files can be uploaded either from your local disk or by specifying a remote sftp / HTTPS location. In both cases, several files or several locations can be selected at once. Please make sure that all files fulfill the [requirements](/prepare-your-data).
-
-
-#### Upload VCF files from your computer
+### Upload VCF files from your computer
 
 When using the file upload, data is uploaded from your local file system to Michigan Imputation Server. By clicking on **Select Files** an open dialog appears where you can select your VCF files:
 
@@ -57,26 +52,11 @@ After you have confirmed your choice, all selected files are listed in the submi
 
 ![](images/upload-data02.png)
 
-
-#### Import VCF files via SFTP
-
-An other convenient way to use your data is by importing it directly from a remote SSH server. This can be achieved by selecting **Secure File Transfer Protocol (SFTP)**.
-
-After clicking on the **Import Files** button, a new dialog appears where you can enter your SFTP credentials and the URLs of your files or folders. A URL consists of the server address followed by the full Unix path. A path can be either point to a folder or to a file. Several paths can be specified in consecutive lines.
-
-![](images/upload-data03.png)
+Please make sure that all files fulfill the [requirements](/prepare-your-data).
 
 
 !!! important
-    Be sure that your SFTP server is **not in a private network** and you are able to establish a connection from outside.
-
-#### Import VCF files via HTTPS
-
-Data can also be imported by using HTTP(S) link. This can be achieved by selecting **URLs (HTTP)**.
-
-After clicking on the **Add URLs** button, a new dialog appears where you can add the links.
-
-![](images/upload-data04.png)		
+    Since version 1.7.2 URL-based uploads (sftp and http) are no longer supported. Please use direct file uploads instead. 
 
 ### Build
 Please select the build of your data. Currently the options **hg19** and **hg38** are supported. Michigan Imputation Server automatically updates the genome positions (liftOver) of your data. All reference panels except TOPMed are based on hg19 coordinates.

files/imputationserver-beagle.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-beagle
 name: Genotype Imputation supporting Beagle (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.2
+version: 1.7.3
 website: https://imputationserver.readthedocs.io
 category:
 

files/imputationserver-hla.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-hla
 name: Genotype Imputation HLA (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.2
+version: 1.7.3
 website: https://imputationserver.readthedocs.io
 category:
 

files/imputationserver-pgs.yaml

@@ -1,7 +1,7 @@
 id: imputationserver-pgs
 name: Genotype Imputation (PGS Calc Integration)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.2
+version: 1.7.3
 website: https://imputationserver.readthedocs.io
 category:
 

files/minimac4.yaml

@@ -1,7 +1,7 @@
 id: imputationserver
 name: Genotype Imputation (Minimac4)
 description: This is the new Michigan Imputation Server Pipeline using <a href="https://github.com/statgen/Minimac4">Minimac4</a>. Documentation can be found <a href="http://imputationserver.readthedocs.io/en/latest/">here</a>.<br><br>If your input data is <b>GRCh37/hg19</b> please ensure chromosomes are encoded without prefix  (e.g. <b>20</b>).<br>If your input data is <b>GRCh38hg38</b> please ensure chromosomes are encoded with prefix 'chr' (e.g. <b>chr20</b>).
-version: 1.7.2
+version: 1.7.3
 website: https://imputationserver.readthedocs.io
 category: