Merge branch 'jdaw/fix-copying-of-cuda-libs' into 'release-v0.7'

Fix CUDAToolkit path to search for libnvrtc

See merge request machine-learning/dorado!1023

CMakeLists.txt

@@ -393,10 +393,10 @@ endif()
 if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
     # CUDA toolkit DLLs we depend on:
     set(VERSIONED_CUDA_LIBS
-        libcublas*.so.*
-        libcudart*.so.*
-        libnvrtc*.so.*
-        libnvToolsExt*.so.*
+        libcublas*.so*
+        libcudart*.so*
+        libnvrtc*.so*
+        libnvToolsExt*.so*
     )
 
     if(CMAKE_SYSTEM_PROCESSOR STREQUAL "aarch64")
@@ -430,7 +430,7 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
             endforeach()
         else()
             # bundle the libraries from the cuda toolkit
-            file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_ROOT}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}")
+            file(GLOB NATIVE_CUDA_LIBS "${CUDAToolkit_TARGET_DIR}/targets/${CMAKE_SYSTEM_PROCESSOR}-linux/lib/${LIB}")
             install(FILES ${NATIVE_CUDA_LIBS} DESTINATION lib COMPONENT redist_libs)
         endif()
     endforeach()

dorado/cli/correct.cpp

@@ -32,9 +32,7 @@ int correct(int argc, char* argv[]) {
     utils::make_torch_deterministic();
     argparse::ArgumentParser parser("dorado", DORADO_VERSION, argparse::default_arguments::help);
     parser.add_description("Dorado read correction tool.");
-    parser.add_argument("reads")
-            .help("Path to a file with reads to correct in FASTQ format.")
-            .nargs(argparse::nargs_pattern::any);
+    parser.add_argument("reads").help("Path to a file with reads to correct in FASTQ format.");
     parser.add_argument("-t", "--threads")
             .help("Combined number of threads for adapter/primer detection and output generation. "
                   "Default uses "