Making an automated pipeline with Windows .exe and scripts with various languages WITHOUT Wine

I have been working on a workflow to process data in order to be used by machine learning models to make predictions. For that I have a few steps in which the first run a windows .exe (https://github.com/mzdb/pwiz-mzdb) and then the others steps are : to modify the previous output to get a matrix in tsv format using a Scala script and some Python scripts to get a final matrix. This last matrix is given to a machine learning model written in Java (Weka).

I know it means 4 different languages to run. I use a windows virtual machine to run the first step and after, I am on Linux environment to run the rest of the workflow.

Now is the time to make an automated pipeline to let users reproduce my results on their computer (both Windows and Linux OS). My first try was to make a Docker Container with Wine to run the first step but unfortunately this was not working... Before integrating this stpe to a docker I tried in Wine alone but the .exe was not able to run because of some software missing that should be there. I have exchanging mails with the developer of the software and he said he has exactly the same error with Wine and he doesn't understand why. Here is the error but I doubt that it could help :

elsa@hp:~/Documents/Elsa_stage/test_raw2mzdb$ WINEPREFIX=~/w3_12_64b_test/ wine raw2mzDB_0.9.10_build20170802/raw2mzDB.exe -i EfaAL1.raw -o EfaAL1.mzdb -f 1-2
0012:fixme:process:SetProcessDEPPolicy (1): stub
0012:fixme:wer:WerSetFlags (2) stub!
0012:fixme:heap:RtlSetHeapInformation (nil) 1 (nil) 0 stub
0019:fixme:process:SetProcessShutdownParameters (00000380, 00000000): partial stub.
001c:fixme:heap:RtlSetHeapInformation 0x240000 0 0x23e830 4 stub
001c:fixme:wer:WerSetFlags (2) stub!
001c:fixme:heap:RtlSetHeapInformation (nil) 1 (nil) 0 stub
0022:fixme:process:SetProcessShutdownParameters (00000380, 00000000): partial stub.
003b:fixme:heap:RtlSetHeapInformation 0xa90000 0 0x22e7f0 4 stub
003b:fixme:heap:RtlSetHeapInformation 0xcb0000 0 0x22e830 4 stub
003b:fixme:process:GetNumaHighestNodeNumber (0x22fa10): semi-stub
003b:fixme:thread:SetThreadStackGuarantee (0x22f9d8): stub
003b:fixme:combase:RoGetParameterizedTypeInstanceIID stub: 4 0x7fd08 0x22b408 0x22bbc0 (nil)
003b:fixme:combase:RoGetParameterizedTypeInstanceIID stub: 3 0x7ff30 0x22b7c8 0x22bf80 (nil)
003b:fixme:combase:RoGetParameterizedTypeInstanceIID stub: 3 0x7ff30 0x22b7c8 0x22bf80 (nil)
003e:fixme:font:get_outline_text_metrics failed to read full_nameW for font L"Ani"!
003e:fixme:nls:GetThreadPreferredUILanguages 00000034, 0x1ae7e690, 0x1ae7e6a0 0x1ae7e610
003e:fixme:nls:get_dummy_preferred_ui_language (0x34 0x1ae7e690 0x1ae7e6a0 0x1ae7e610) returning a dummy value (current locale)
003e:fixme:nls:GetThreadPreferredUILanguages 00000034, 0x1ae7e680, 0x1ae7e690 0x1ae7e600
003e:fixme:nls:get_dummy_preferred_ui_language (0x34 0x1ae7e680 0x1ae7e690 0x1ae7e600) returning a dummy value (current locale)
003e:err:ole:marshal_object Failed to create an IRpcStubBuffer from IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
003b:err:ole:ClientIdentity_QueryMultipleInterfaces IRemUnknown_RemQueryInterface failed with error 0x80004002
003b:err:ole:PSFacBuf_CreateProxy Could not commit pages for proxy thunks
003b:err:ole:proxy_manager_create_ifproxy Could not create proxy for interface {06f53853-e43c-4f30-9e5f-d1b3668f0c3c}, error 0x8007000e
003b:err:ole:ClientIdentity_QueryMultipleInterfaces Failed to get pointer to interface {06f53853-e43c-4f30-9e5f-d1b3668f0c3c}
003e:err:ole:marshal_object Failed to create an IRpcStubBuffer from IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
003b:err:ole:ClientIdentity_QueryMultipleInterfaces IRemUnknown_RemQueryInterface failed with error 0x80004002
003b:err:ole:PSFacBuf_CreateProxy Could not commit pages for proxy thunks
003b:err:ole:proxy_manager_create_ifproxy Could not create proxy for interface {e7cf6760-11cd-4260-b5b0-fce2ad97547b}, error 0x8007000e
003b:err:ole:ClientIdentity_QueryMultipleInterfaces Failed to get pointer to interface {e7cf6760-11cd-4260-b5b0-fce2ad97547b}
003e:err:ole:marshal_object Failed to create an IRpcStubBuffer from IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
003b:err:ole:ClientIdentity_QueryMultipleInterfaces IRemUnknown_RemQueryInterface failed with error 0x80004002
003b:err:ole:PSFacBuf_CreateProxy Could not commit pages for proxy thunks
003b:err:ole:proxy_manager_create_ifproxy Could not create proxy for interface {19a00b1e-1559-42b1-9a46-08a5e599edee}, error 0x8007000e
003b:err:ole:ClientIdentity_QueryMultipleInterfaces Failed to get pointer to interface {19a00b1e-1559-42b1-9a46-08a5e599edee}
003e:err:ole:marshal_object Failed to create an IRpcStubBuffer from IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
003b:err:ole:ClientIdentity_QueryMultipleInterfaces IRemUnknown_RemQueryInterface failed with error 0x80004002
003b:err:ole:PSFacBuf_CreateProxy Could not commit pages for proxy thunks
003b:err:ole:proxy_manager_create_ifproxy Could not create proxy for interface {55a25ff7-f437-471f-909a-d7f2b5930805}, error 0x8007000e
003b:err:ole:ClientIdentity_QueryMultipleInterfaces Failed to get pointer to interface {55a25ff7-f437-471f-909a-d7f2b5930805}
003e:err:ole:marshal_object Failed to create an IRpcStubBuffer from IPSFactory for {00000126-0000-0000-c000-000000000046} with error 0x80004002
003b:err:ole:ClientIdentity_QueryMultipleInterfaces IRemUnknown_RemQueryInterface failed with error 0x80004002
003b:err:ole:PSFacBuf_CreateProxy Could not commit pages for proxy thunks
003b:err:ole:proxy_manager_create_ifproxy Could not create proxy for interface {11b488a0-69b1-41fc-a660-fe8df2a31f5b}, error 0x8007000e
003b:err:ole:ClientIdentity_QueryMultipleInterfaces Failed to get pointer to interface {11b488a0-69b1-41fc-a660-fe8df2a31f5b}
E0625 12:36:10.297827    59 raw2mzDB.cpp:537] [ThermoRawFile] [RawFile::ctor] Unable to initialize XRawfile; is MSFileReader installed? Reading Thermo RAW files requires MSFileReader to be installed. It is available for download at:
http://sjsupport.thermofinnigan.com/public/detail.asp?id=703
F0625 12:36:10.297992    59 raw2mzDB.cpp:538] This a fatal error. Exiting...
*** Check failure stack trace: ***
wine: Unhandled exception 0x40000015 in thread 3b at address 0x797a61c9 (thread 003b), starting debugger...
003b:fixme:process:FlushProcessWriteBuffers : stub
003b:fixme:msvcrt:__clean_type_info_names_internal (0xa55658) stub

So my question is, do you know another way to make an automated pipeline in which I can run an windows .exe and various scripts using various languages (without Wine) ? I can't use a virtual machine since I can't re-distribute windows everywhere.

Thank you for your help !

Elsa