Fixed bugs related to documentation urls.

docs/markdown_files/configuration.md

@@ -163,4 +163,4 @@ displaying is limited to the samples that the laboratory that user belongs to.
 
 As the process of user creation is part of the maintenance activity we have
 create a separate chapter inside FAQ. To check the documentation for user creation
-click on  a new user now [How to create new user](createNewUserAccount.md)
+click on  a new user now [How to create new user](../create_new_user.md)

docs/markdown_files/description.md

@@ -28,5 +28,5 @@ The website stores all the processed data and metadata, and allows the visualiza
 
 
 ## Relecov-tools
-relecov tools is a python package with helper functions for data management in the project. Read more [here](relecov_tools.md)
+relecov tools is a python package with helper functions for data management in the project. Read more [here](../relecov_tools.md)
 

docs/markdown_files/index.md

@@ -15,10 +15,10 @@
     - [relecov-tools](relecov_tools.md)
 
 - Intranet
-    - [Overview](intranetOverview.md)
-    - [Upload Metadata](intranetUploadMetadata.md)
-    - [Contact data](intranetContactData.md)
-    - [Sample Processing](sampleProcessing.md)
+    - [Overview](intranet_overview.md)
+    - [Upload Metadata](intranet_upload_metadata.md)
+    - [Contact data](intranet_contact_data.md)
+    - [Sample Processing](intranet_received_samples.md)
 
 - Dashboards
     - [Variant dashboard](variant_dashboard.md)

docs/markdown_files/intranet_overview.md

@@ -19,7 +19,7 @@ To access Intranet click on the "Intranet" button.
 If you do not have login credential yet, contact with your manager to request
 them for you.
 
-For **admin** user follow the instructions provide in [Create new user](/documentation/createNewUSer) to add new user.
+For **admin** user follow the instructions provide in [Create new user](../create_new_user.md) to add new user.
 
 ---
 

docs/markdown_files/intranet_upload_metadata.md

@@ -12,7 +12,7 @@ The option 1 (Filling the information in metadata lab form) you do not need to p
 
 Option 2 (Upload Metadata Excel file). You need to fill in advance the Metadata Lab excel file
 
-The last alternative (Using SFTP server) is not available from relecov. You need to upload the Excel metadata file to the sftp server. Detailed information how to do upload this file is described in [How to fill metadata lab excel](/documentation/metadataLabExcel)
+The last alternative (Using SFTP server) is not available from relecov. You need to upload the Excel metadata file to the sftp server. Detailed information how to do upload this file is described in [How to fill metadata lab excel](../metadata_lab_excel.md)
 
 
 If you decide to use the alternative 1 or 2, click on the left side menu the "Upload Metadata" link, to display the page to upload your metadata.
@@ -46,7 +46,7 @@ As you will see in this form there are 3 types of data:
 - Select. Press on the cell to display and choose the option that fit in your case.
 
 ---
-If you have any doubt for any field you can have a look to [How to fill metadata lab excel](/documentation/metadataLabExcel)
+If you have any doubt for any field you can have a look to [How to fill metadata lab excel](../metadata_lab_excel.md)
 
 ---
 

docs/markdown_files/metadata.md

@@ -26,4 +26,4 @@ Ph4age classification fields have been extended according to their nature:
 8. Pathogen diagnostic testing
 9. Public databases
 
-An excel file has been generated including the fields belonging to the labs to facilitate its collection and upload to the platform. [See next section](metadata_lab_excel.md)
+An excel file has been generated including the fields belonging to the labs to facilitate its collection and upload to the platform. [See next section](../metadata_lab_excel.md)

docs/markdown_files/metadata_lab_excel.md

@@ -1,13 +1,13 @@
 # Excel metadata: data provided by the microbiology labs
 
 ## Excel description
-We provide an excel that gathers all the fields that need to be provided by the labs in the network. The excel can be downloaded from the platform intranet in the [Upload section](upload_metadata_lab.md).
+We provide an excel that gathers all the fields that need to be provided by the labs in the network. The excel can be downloaded from the platform intranet in the [Upload section](../intranet_upload_metadata.md).
 
    - First sheet (Overview) shows the description of each field with an example of how it has to be filled, also indicating which fields are mandatory.
    - Second sheet (METADATA_LAB) needs is the sheet you need to modify. First line includes notes for clarification, second line includes an example, third line a description of the field, and forth line is the field name. You must not modify or delete any of this four lines, you only have to start filling the information of the first sample in the fifth line, creating one line for each sample. Fields with limited options have a dropdown list where you can select the appropiate value for your sample. Please use the provided options or ask for adding a new one.
    - Third sheet (DATA VALIDATION) includes the options available for each field. If you need additional options please contact us ([email protected])
 
-Your lab can filled this excel manually, most of the fields belong the same for most of your samples, as most of the fields describes the sequencing protocol. But, if your lab have programming skills and you want this excel to be filled automatically from other sources (other excel files, a database, etc) we provide a python module (*homogeneizer*) enclosed in [relecov-tools package](relecov_tools.md).
+Your lab can filled this excel manually, most of the fields belong the same for most of your samples, as most of the fields describes the sequencing protocol. But, if your lab have programming skills and you want this excel to be filled automatically from other sources (other excel files, a database, etc) we provide a python module (*homogeneizer*) enclosed in [relecov-tools package](../relecov_tools.md).
 
 **Table 1.**  Overview of fields that must be filled by the microbiology labs.