diff --git a/README.md b/README.md
index 2e54ddc..0c78493 100644
--- a/README.md
+++ b/README.md
@@ -183,6 +183,14 @@ A file called `openapi.generated.json` would be created with the endpoints infor
 ATOM_TOOLS_OPENAPI_FILENAME=openapi.json atom usages --extract-endpoints -o app.atom --slice-outfile usages.json -l ruby .
 ```
 
+Container-based invocation:
+
+```shell
+docker run --rm -v /tmp:/tmp -e ATOM_TOOLS_OPENAPI_FILENAME=openapi.json -v $(pwd):/app:rw -t ghcr.io/appthreat/atom atom usages --extract-endpoints -l ruby -o /app/app.atom -s /app/usages.slices.json /app
+# podman run --rm -v /tmp:/tmp -e ATOM_TOOLS_OPENAPI_FILENAME=openapi.json -v $(pwd):/app:rw -t ghcr.io/appthreat/atom atom usages --extract-endpoints -l ruby -o /app/app.atom -s /app/usages.slices.json /app
+```
+
+
 ### Export atom to graphml or dot format
 
 It is possible to export each method along with data dependencies in an atom to graphml or dot format. Simply pass `--export` to enable this feature.
diff --git a/src/main/scala/io/appthreat/atom/Atom.scala b/src/main/scala/io/appthreat/atom/Atom.scala
index 19cff27..94476dc 100644
--- a/src/main/scala/io/appthreat/atom/Atom.scala
+++ b/src/main/scala/io/appthreat/atom/Atom.scala
@@ -366,10 +366,14 @@ object Atom:
               val openapiFileName =
                   sys.env.getOrElse("ATOM_TOOLS_OPENAPI_FILENAME", "openapi.generated.json")
               val openapiFormat = sys.env.getOrElse("ATOM_TOOLS_OPENAPI_FORMAT", "openapi3.1.0")
+              val atomToolsWorkDir =
+                  sys.env.getOrElse("ATOM_TOOLS_WORK_DIR", config.inputPath.parent.pathAsString)
+              println(s"atom-tools convert -i ${config.outputSliceFile} -t ${config.language} -f ${openapiFormat} -o ${config
+                      .inputPath.pathAsString}${java.io.File.separator}${openapiFileName}")
               val result = ExternalCommand.run(
-                s"atom-tools convert -i ${config.outputSliceFile} -t ${config.language} -f ${openapiFormat} -q -o ${config
+                s"atom-tools convert -i ${config.outputSliceFile} -t ${config.language} -f ${openapiFormat} -o ${config
                         .inputPath.pathAsString}${java.io.File.separator}${openapiFileName}",
-                "."
+                atomToolsWorkDir
               )
               result match
                 case Success(_) =>
@@ -378,6 +382,7 @@ object Atom:
                     println(
                       s"Failed to run atom-tools. Use the atom container image or perform 'pip install atom-tools' and re-run this command. Exception: ${exception.getMessage}"
                     )
+            end if
         case _: ReachablesConfig =>
             saveSlice(config.outputSliceFile, sliceCpg(ag).map(_.toJson))
         case x: AtomParseDepsConfig =>