diff --git a/pipeline-runner/DESCRIPTION b/pipeline-runner/DESCRIPTION
index fbc8116e..dc0bf5ff 100644
--- a/pipeline-runner/DESCRIPTION
+++ b/pipeline-runner/DESCRIPTION
@@ -13,7 +13,6 @@ License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
 Depends: 
     R (>= 4.2.0)
 Imports:
-    batchelor (== 1.12.1),
     covr,
     magrittr,
     data.table
diff --git a/pipeline-runner/renv.lock b/pipeline-runner/renv.lock
index 5613bbd0..beee1bea 100644
--- a/pipeline-runner/renv.lock
+++ b/pipeline-runner/renv.lock
@@ -833,13 +833,13 @@
     },
     "batchelor": {
       "Package": "batchelor",
-      "Version": "1.12.1",
+      "Version": "1.12.3",
       "Source": "Bioconductor",
       "git_url": "https://git.bioconductor.org/packages/batchelor",
       "git_branch": "RELEASE_3_15",
-      "git_last_commit": "685db2e",
-      "git_last_commit_date": "2022-05-25",
-      "Hash": "ae6f9b5b90d5f012249f85c8ecd560f7",
+      "git_last_commit": "94788f9",
+      "git_last_commit_date": "2022-06-22",
+      "Hash": "f03c96a4e54ce90fcdf4c7354e4c83a6",
       "Requirements": [
         "BiocGenerics",
         "BiocNeighbors",
@@ -1094,13 +1094,13 @@
     },
     "desc": {
       "Package": "desc",
-      "Version": "1.3.0",
+      "Version": "1.4.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "b6963166f7f10b970af1006c462ce6cd",
+      "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21",
       "Requirements": [
         "R6",
-        "crayon",
+        "cli",
         "rprojroot"
       ]
     },
@@ -2014,17 +2014,18 @@
     },
     "pkgload": {
       "Package": "pkgload",
-      "Version": "1.2.1",
+      "Version": "1.3.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "463642747f81879e6752485aefb831cf",
+      "Hash": "6b0c222c5071efe0f3baf3dae9aa40e2",
       "Requirements": [
         "cli",
         "crayon",
         "desc",
+        "fs",
+        "glue",
         "rlang",
         "rprojroot",
-        "rstudioapi",
         "withr"
       ]
     },
@@ -2166,10 +2167,10 @@
     },
     "remotes": {
       "Package": "remotes",
-      "Version": "2.4.0",
+      "Version": "2.4.2",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "a85ebb35721573b196317b49ddd2dfe4",
+      "Hash": "227045be9aee47e6dda9bb38ac870d67",
       "Requirements": []
     },
     "renv": {
@@ -2285,10 +2286,10 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "1.0.2",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "04884d9a75d778aca22c7154b8333ec9",
+      "Hash": "4ed1f8336c8d52c3e750adcdc57228a7",
       "Requirements": []
     },
     "rpart": {
@@ -2307,14 +2308,6 @@
       "Hash": "249d8cd1e74a8f6a26194a91b47f21d1",
       "Requirements": []
     },
-    "rstudioapi": {
-      "Package": "rstudioapi",
-      "Version": "0.13",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "06c85365a03fdaf699966cc1d3cf53ea",
-      "Requirements": []
-    },
     "rsvd": {
       "Package": "rsvd",
       "Version": "1.0.5",
@@ -2517,13 +2510,13 @@
     },
     "scuttle": {
       "Package": "scuttle",
-      "Version": "1.6.2",
+      "Version": "1.6.3",
       "Source": "Bioconductor",
       "git_url": "https://git.bioconductor.org/packages/scuttle",
       "git_branch": "RELEASE_3_15",
-      "git_last_commit": "afdfc55",
-      "git_last_commit_date": "2022-05-13",
-      "Hash": "47027fcc659e73ae827d4cebf54467e9",
+      "git_last_commit": "df23680",
+      "git_last_commit_date": "2022-08-23",
+      "Hash": "30e9a1169ef27c0bc373117773b15bec",
       "Requirements": [
         "BiocGenerics",
         "BiocParallel",