Upload and download
You can upload files only If you have an organization admin or organization member permission role at an organization or a guest role (with read/write role type) at a project.
Upload Sample
The upload samples function provides a quick way to upload one or more sample files.
The function guides you along the steps: (1) Select organization, (2) select or create a project, and (3) select files and finally, (4) you can select apps to run (optional step).
There are two types of uploads:
Bulk upload: In bulk upload mode, the system reads the sample name, lane number, and read number information from the file names based on the naming convention.
You can define your naming convention by clicking the “File naming convention” bar.
Single upload: In case of a single upload, the user should add the sample name and set the lane and read number on the screen:
https://biotia.atlassian.net/wiki/spaces/GPUD/pages/189071364
Other file types - Upload manually
In the case of other file types, you can’t use the “Upload samples” function. Instead, you can do it on the folder or file level:
Create a folder
You can create a folder on your sample page:
Or You can do the same on the project folders screen:
You can create an empty folder and upload files later, or you can create a folder and upload file(s) in one step:
Upload file
Finally, you can upload a file from your folder page:
Download files
You can download files from the folder page from the file list:
Bulk download
It is possible to download more files together based on your filter on file, folder, or sample.
Start the function:
You can start the function from the file, folder, or sample list headers:
Filters
In the first modal window You can set the followings:
Extension: You can define more extensions If It’s needed.
File version: If you select the “Latest versions”, you will get only the last, current version of the files. If you select “All versions” you will get the latest and every previous version of the files.
File name: If you switch the toggle you can define the patterns for the file names. For example:
Folder name: If you switch the toggle you can define the patterns for the folder names. (Available only If You start the bulk download from the folder or the sample level.)
Sample name: If You switch the toggle You can define the patterns for the sample names. (Available only If You start the bulk download from the sample level.)
All conditions must be met at the same time. It means the logical operand between the conditions is “AND”, except If Those conditions are in one row. For example: File names should contain “lane_1” OR “lane_2” text.
Summary
On the second, last screen - before the download - You can check the sum of the file size, and the number of files that will be downloaded.
Click on the “Download” button to get the files.
If You download more files from more folders and samples, You will get the files this way:
It helps You to know the precise file position in the project data hierarchy.
Uploading and Downloading from the Command Line
You can upload and download files from the command line. Please take a look at the documentation here.
Sample files for upload wizard tutorial:
