diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 9914d7e7c8c..f6673b02d82 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -93,14 +93,14 @@ pytest==7.1.3 ; python_version >= "3.7" and python_version < "3.11"
 python-dateutil==2.8.2 ; python_version >= "3.7" and python_version < "3.11"
 python-irodsclient==1.1.5 ; python_version >= "3.7" and python_version < "3.11"
 pytz==2022.5 ; python_version >= "3.7" and python_version < "3.11"
-rdflib==6.0.2 ; python_version >= "3.7" and python_version < "3.11"
+rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.11"
 recommonmark==0.7.1 ; python_version >= "3.7" and python_version < "3.11"
 requests==2.28.1 ; python_version >= "3.7" and python_version < "3.11"
 responses==0.22.0 ; python_version >= "3.7" and python_version < "3.11"
 rfc3986[idna2008]==1.5.0 ; python_version >= "3.7" and python_version < "3.11"
-ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.7"
-ruamel-yaml==0.17.17 ; python_version >= "3.7" and python_version < "3.11"
-schema-salad==8.3.20221016151607 ; python_version >= "3.7" and python_version < "3.11"
+ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
+ruamel-yaml==0.17.21 ; python_version >= "3.7" and python_version < "3.11"
+schema-salad==8.3.20221028160159 ; python_version >= "3.7" and python_version < "3.11"
 scipy==1.7.3 ; python_version >= "3.7" and python_version < "3.11"
 selenium==4.5.0 ; python_version >= "3.7" and python_version < "3.11"
 setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.11"
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 8ed626cfdc2..36d73d44011 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -46,7 +46,9 @@ colorama==0.4.5 ; python_version >= "3.7" and python_version < "3.11" and platfo
 coloredlogs==15.0.1 ; python_version >= "3.7" and python_version < "3.11"
 commonmark==0.9.1 ; python_version >= "3.7" and python_version < "3.11"
 cryptography==38.0.3 ; python_version >= "3.7" and python_version < "3.11"
-cwltool==3.1.20211107152837 ; python_version >= "3.7" and python_version < "3.11"
+cwl-upgrader==1.2.4 ; python_version >= "3.7" and python_version < "3.11"
+cwl-utils==0.20 ; python_version >= "3.7" and python_version < "3.11"
+cwltool==3.1.20221109155812 ; python_version >= "3.7" and python_version < "3.11"
 decorator==5.1.1 ; python_version >= "3.7" and python_version < "3.11"
 defusedxml==0.7.1 ; python_version >= "3.7" and python_version < "3.11"
 deprecation==2.1.0 ; python_version >= "3.7" and python_version < "3.11"
@@ -138,7 +140,7 @@ python3-openid==3.2.0 ; python_version >= "3.7" and python_version < "3.11"
 pytz==2022.5 ; python_version >= "3.7" and python_version < "3.11"
 pyyaml==6.0 ; python_version >= "3.7" and python_version < "3.11"
 pyzmq==24.0.1 ; python_version >= "3.7" and python_version < "3.11"
-rdflib==6.0.2 ; python_version >= "3.7" and python_version < "3.11"
+rdflib==6.2.0 ; python_version >= "3.7" and python_version < "3.11"
 refgenconf==0.12.2 ; python_version >= "3.7" and python_version < "3.11"
 repoze-lru==0.7 ; python_version >= "3.7" and python_version < "3.11"
 requests-oauthlib==1.3.1 ; python_version >= "3.7" and python_version < "3.11"
@@ -148,9 +150,9 @@ rich==12.6.0 ; python_version >= "3.7" and python_version < "3.11"
 rocrate==0.7.0 ; python_version >= "3.7" and python_version < "3.11"
 routes==2.5.1 ; python_version >= "3.7" and python_version < "3.11"
 rsa==4.9 ; python_version >= "3.7" and python_version < "3.11"
-ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.10" and python_version >= "3.7"
-ruamel-yaml==0.17.17 ; python_version >= "3.7" and python_version < "3.11"
-schema-salad==8.3.20221016151607 ; python_version >= "3.7" and python_version < "3.11"
+ruamel-yaml-clib==0.2.7 ; platform_python_implementation == "CPython" and python_version < "3.11" and python_version >= "3.7"
+ruamel-yaml==0.17.21 ; python_version < "3.11" and python_version >= "3.7"
+schema-salad==8.3.20221028160159 ; python_version >= "3.7" and python_version < "3.11"
 setuptools-scm==5.0.2 ; python_version >= "3.7" and python_version < "3.11"
 setuptools==65.5.0 ; python_version >= "3.7" and python_version < "3.11"
 shellescape==3.8.1 ; python_version >= "3.7" and python_version < "3.11"
diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
index 05364f69fde..7f2db40b020 100644
--- a/packages/tool_util/setup.cfg
+++ b/packages/tool_util/setup.cfg
@@ -57,7 +57,7 @@ console_scripts =
 
 [options.extras_require]
 cwl =
-    cwltool==3.1.20211107152837
+    cwltool==3.1.20221109155812
 mulled =
     jinja2
     Whoosh
diff --git a/pyproject.toml b/pyproject.toml
index 71b8c0c519b..7e7d1542c28 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,7 +45,7 @@ Cheetah3 = "!=3.2.6.post2"  # yanked release, https://github.com/python-poetry/p
 cloudauthz = "==0.6.0"
 cloudbridge = "*"
 circus = "*"
-cwltool = "==3.1.20211107152837"
+cwltool = "==3.1.20221109155812"
 dictobj = "*"
 dnspython = "*"
 docutils = "!=0.17, !=0.17.1"