adding documentation for certificate change problems

docs/usage.rst

@@ -148,6 +148,25 @@ remove all the flags:
 
 and rerun dissectBCL. Note that an existing demuxSheet in the folder won't be overwritten, allowing you to jump in.
 
+Issues with Parkour verification
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+In this case (which is rare as it's caused by changing the certificate provider and it is not commonly listed), the certificate issuer is not recognized as dissect throws this error:
+
+.. code-block:: console
+
+    requests.exceptions.SSLError: HTTPSConnectionPool(host='parkour.ie-freiburg.mpg.de', port=443): Max retries exceeded with url: 
+    /api/analysis_list/analysis_list/?flowcell_id=XXXXXXXXX (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate 
+    verify failed: unable to get local issuer certificate (_ssl.c:1007)')))
+
+then, the new certificate needs to be added in the system (i.e. for CenOS 7, copying it to /etc/pki/ca-trust/source/anchors/ and run "update-ca-trust") and append the content to "cacert.pem" as certifi uses this file to check the issuer.
+Python requests uses certifi to verify SSL connections, however, it is not using the system certificates and uses their own file.
+To find where is that file, it can be requested as:
+
+.. code-block:: console
+    
+    python -m certifi
+    
+
 Other issues
 ^^^^^^^^^^^^
 It can happen that the pipeline just crashes. A point of entry there would be to have a look at the log files. These are written per flowcell.