diff --git a/requirements.in b/requirements.in
deleted file mode 100644
index 6474c9c..0000000
--- a/requirements.in
+++ /dev/null
@@ -1,8 +0,0 @@
-# This file is part of REANA.
-# Copyright (C) 2020, 2022, 2023 CERN.
-#
-# REANA is free software; you can redistribute it and/or modify it
-# under the terms of the MIT License; see LICENSE file for more details.
-
-jq==1.7.0
-pygraphviz==1.8
diff --git a/requirements.txt b/requirements.txt
index ceca060..8d90f3c 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,7 +2,7 @@
 # This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
-#    pip-compile --annotation-style=line --output-file=requirements.txt requirements.in setup.py
+#    pip-compile --annotation-style=line --extra=jq,pygraphviz --output-file=requirements.txt setup.py
 #
 adage==0.11.0             # via reana-commons, reana-workflow-engine-yadage (setup.py), yadage
 amqp==5.2.0               # via kombu
@@ -24,7 +24,7 @@ graphviz==0.20.3          # via reana-workflow-engine-yadage (setup.py)
 idna==3.7                 # via jsonschema, requests
 importlib-resources==6.4.0  # via swagger-spec-validator
 isoduration==20.11.0      # via jsonschema
-jq==1.7.0 ;               # via -r requirements.in, packtivity, yadage
+jq==1.7.0                 # via packtivity, reana-workflow-engine-yadage (setup.py), yadage
 jsonpath-rw==1.4.0        # via packtivity, yadage
 jsonpointer==3.0.0        # via jsonschema, packtivity, yadage
 jsonref==1.1.0            # via bravado-core, packtivity, yadage, yadage-schemas
@@ -41,7 +41,7 @@ ply==3.11                 # via jsonpath-rw
 psutil==6.0.0             # via yadage
 pydot==3.0.1              # via reana-workflow-engine-yadage (setup.py)
 pydotplus==2.0.2          # via reana-workflow-engine-yadage (setup.py)
-pygraphviz==1.8           # via -r requirements.in
+pygraphviz==1.8           # via reana-workflow-engine-yadage (setup.py)
 pyparsing==3.1.2          # via pydot, pydotplus
 pyrsistent==0.20.0        # via jsonschema
 python-dateutil==2.9.0.post0  # via arrow, bravado, bravado-core