diff --git a/CHANGELOG.md b/CHANGELOG.md
index 46b8447d..c7d8cb36 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# openpipelines 4.0.1
+
+## BUG FIXES
+
+* Fix parsing of CSV's failing when using remote paths (S3), causing an `InvocationTargetException` error (PR #1133).
+
 # openpipelines 4.0.0
 
 ## BREAKING CHANGES
diff --git a/_viash.yaml b/_viash.yaml
index 49fb8290..dd581320 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,5 @@
 viash_version: 0.9.4
-version: v4.0.0
+version: v4.0.1
 source: src
 target: target
 # Note: this causes the docker images to be renamed
diff --git a/src/workflows/annotation/harmony_knn/main.nf b/src/workflows/annotation/harmony_knn/main.nf
index 935ab3a2..e49e581a 100644
--- a/src/workflows/annotation/harmony_knn/main.nf
+++ b/src/workflows/annotation/harmony_knn/main.nf
@@ -50,8 +50,11 @@ workflow run_wf {
         )
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
-        
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         types.collect{ dat ->
           // def new_id = id + "_" + dat.name
           def new_id = id // it's okay because the channel will get split up anyways
@@ -187,7 +190,11 @@ workflow run_wf {
                 ]
                 return [id, new_state]
             }
-            def files = readCsv(state.output_files.toUriString())
+            def csv = state.output_files.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+            def header = csv.head()
+            def files = csv.tail().collect { row ->
+                [header, row].transpose().collectEntries()
+            }
             def query_file = files.findAll{ dat -> dat.name == 'query' }
             assert query_file.size() == 1, 'there should only be one query file'
             def reference_file = files.findAll{ dat -> dat.name == 'reference' }
diff --git a/src/workflows/annotation/scvi_knn/main.nf b/src/workflows/annotation/scvi_knn/main.nf
index a4c8cc57..4e98084e 100644
--- a/src/workflows/annotation/scvi_knn/main.nf
+++ b/src/workflows/annotation/scvi_knn/main.nf
@@ -53,7 +53,11 @@ workflow run_wf {
       )
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         
         types.collect{ dat ->
           // def new_id = id + "_" + dat.name
@@ -191,7 +195,11 @@ workflow run_wf {
             ]
             return [id, new_state]
           }
-          def files = readCsv(state.output_files.toUriString())
+          def csv = state.output_files.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+          def header = csv.head()
+          def files = csv.tail().collect { row ->
+              [header, row].transpose().collectEntries()
+          }
           def query_file = files.findAll{ dat -> dat.name == 'query' }
           assert query_file.size() == 1, 'there should only be one query file'
           def reference_file = files.findAll{ dat -> dat.name == 'reference' }
diff --git a/src/workflows/ingestion/cellranger_multi/main.nf b/src/workflows/ingestion/cellranger_multi/main.nf
index d432e293..bdb8b09a 100644
--- a/src/workflows/ingestion/cellranger_multi/main.nf
+++ b/src/workflows/ingestion/cellranger_multi/main.nf
@@ -117,7 +117,11 @@ workflow run_wf {
   output_ch = h5mu_stub_ch.concat(h5mu_ch)
     | flatMap {id, state ->
       def h5mu_list = state.output_h5mu
-      def samples = readCsv(state.sample_csv.toUriString())
+      def csv = state.sample_csv.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+      def header = csv.head()
+      def samples = csv.tail().collect { row ->
+          [header, row].transpose().collectEntries()
+      }
       println "Samples: $samples" 
       def result = h5mu_list.collect{ h5mu_file ->
         println "H5mu: ${h5mu_file}, getName: ${h5mu_file.getName()}"
diff --git a/src/workflows/multiomics/process_batches/main.nf b/src/workflows/multiomics/process_batches/main.nf
index 9da48a3e..8b35c869 100644
--- a/src/workflows/multiomics/process_batches/main.nf
+++ b/src/workflows/multiomics/process_batches/main.nf
@@ -43,7 +43,11 @@ workflow run_wf {
       // by reading the output csv (the csv contains 1 line per output file)
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         
         types.collect{ dat ->
           def new_id = state.original_id + "_${dat.name}" // Make a unique ID by appending the modality name.
diff --git a/src/workflows/multiomics/process_samples/main.nf b/src/workflows/multiomics/process_samples/main.nf
index 7bacc1c2..1e3b8ecc 100644
--- a/src/workflows/multiomics/process_samples/main.nf
+++ b/src/workflows/multiomics/process_samples/main.nf
@@ -52,7 +52,11 @@ workflow run_wf {
       )
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         
         types.collect{ dat ->
           // def new_id = id + "_" + dat.name
diff --git a/target/_private/executable/filter/delimit_counts/.config.vsh.yaml b/target/_private/executable/filter/delimit_counts/.config.vsh.yaml
index b656ef04..51431dd8 100644
--- a/target/_private/executable/filter/delimit_counts/.config.vsh.yaml
+++ b/target/_private/executable/filter/delimit_counts/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "delimit_counts"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -217,7 +217,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -258,11 +258,11 @@ build_info:
   output: "target/_private/executable/filter/delimit_counts"
   executable: "target/_private/executable/filter/delimit_counts/delimit_counts"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/executable/filter/delimit_counts/delimit_counts b/target/_private/executable/filter/delimit_counts/delimit_counts
index 785b5ebb..c7f0e52f 100755
--- a/target/_private/executable/filter/delimit_counts/delimit_counts
+++ b/target/_private/executable/filter/delimit_counts/delimit_counts
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# delimit_counts v4.0.0
+# delimit_counts v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component filter delimit_counts"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:41Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "delimit_counts v4.0.0"
+  echo "delimit_counts v4.0.1"
   echo ""
   echo "Turns an .obs column containing count values into a boolean column based on"
   echo "thresholds."
@@ -680,7 +680,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "delimit_counts v4.0.0"
+            echo "delimit_counts v4.0.1"
             exit
             ;;
         --input)
@@ -864,7 +864,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_counts:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_counts:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml
index 29bea659..8fdf85e5 100644
--- a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml
+++ b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_mudata_obs_to_tiledb"
 namespace: "tiledb"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -243,7 +243,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -288,11 +288,11 @@ build_info:
   output: "target/_private/executable/tiledb/move_mudata_obs_to_tiledb"
   executable: "target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -322,7 +322,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb
index 7568f8d4..9a88fecf 100755
--- a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb
+++ b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# move_mudata_obs_to_tiledb v4.0.0
+# move_mudata_obs_to_tiledb v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component tiledb move_mudata_obs_to_tiledb"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "move_mudata_obs_to_tiledb v4.0.0"
+  echo "move_mudata_obs_to_tiledb v4.0.1"
   echo ""
   echo "Move .obs columns from a MuData modality to an existing tileDB database."
   echo "The .obs keys should not exist in the database yet; and the observations from"
@@ -686,7 +686,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "move_mudata_obs_to_tiledb v4.0.0"
+            echo "move_mudata_obs_to_tiledb v4.0.1"
             exit
             ;;
         --input_uri)
@@ -904,7 +904,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obs_to_tiledb:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obs_to_tiledb:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml
index 57c9242a..ecee9f39 100644
--- a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml
+++ b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_mudata_obsm_to_tiledb"
 namespace: "tiledb"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -220,7 +220,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -265,11 +265,11 @@ build_info:
   output: "target/_private/executable/tiledb/move_mudata_obsm_to_tiledb"
   executable: "target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -299,7 +299,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb
index 7094c285..53d6d9d7 100755
--- a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb
+++ b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# move_mudata_obsm_to_tiledb v4.0.0
+# move_mudata_obsm_to_tiledb v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component tiledb move_mudata_obsm_to_tiledb"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "move_mudata_obsm_to_tiledb v4.0.0"
+  echo "move_mudata_obsm_to_tiledb v4.0.1"
   echo ""
   echo "Move .obsm items from a MuData modality to an existing tileDB database."
   echo "The .obsm keys should not exist in the database yet; and the observations from"
@@ -675,7 +675,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "move_mudata_obsm_to_tiledb v4.0.0"
+            echo "move_mudata_obsm_to_tiledb v4.0.1"
             exit
             ;;
         --input_uri)
@@ -871,7 +871,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsm_to_tiledb:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsm_to_tiledb:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml
index 9f746c04..5b4b236b 100644
--- a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml
+++ b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_mudata_obsp_to_tiledb"
 namespace: "tiledb"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -220,7 +220,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -265,11 +265,11 @@ build_info:
   output: "target/_private/executable/tiledb/move_mudata_obsp_to_tiledb"
   executable: "target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -299,7 +299,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb
index 7bff450f..3f3281f7 100755
--- a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb
+++ b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# move_mudata_obsp_to_tiledb v4.0.0
+# move_mudata_obsp_to_tiledb v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component tiledb move_mudata_obsp_to_tiledb"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "move_mudata_obsp_to_tiledb v4.0.0"
+  echo "move_mudata_obsp_to_tiledb v4.0.1"
   echo ""
   echo "Move .obsp items from a MuData modality to an existing tileDB database."
   echo "The .obsp keys should not exist in the database yet; and the observations from"
@@ -675,7 +675,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "move_mudata_obsp_to_tiledb v4.0.0"
+            echo "move_mudata_obsp_to_tiledb v4.0.1"
             exit
             ;;
         --input_uri)
@@ -871,7 +871,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsp_to_tiledb:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsp_to_tiledb:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml b/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml
index 6972c391..b831ed12 100644
--- a/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml
+++ b/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "delimit_counts"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -217,7 +217,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -258,11 +258,11 @@ build_info:
   output: "target/_private/nextflow/filter/delimit_counts"
   executable: "target/_private/nextflow/filter/delimit_counts/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/nextflow/filter/delimit_counts/main.nf b/target/_private/nextflow/filter/delimit_counts/main.nf
index 0f7c7fd2..017d6fd1 100644
--- a/target/_private/nextflow/filter/delimit_counts/main.nf
+++ b/target/_private/nextflow/filter/delimit_counts/main.nf
@@ -1,4 +1,4 @@
-// delimit_counts v4.0.0
+// delimit_counts v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "delimit_counts",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3309,7 +3309,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3365,12 +3365,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_private/nextflow/filter/delimit_counts",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3395,7 +3395,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3940,7 +3940,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/delimit_counts",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/_private/nextflow/filter/delimit_counts/nextflow.config b/target/_private/nextflow/filter/delimit_counts/nextflow.config
index 4cf8141f..cff4fa2e 100644
--- a/target/_private/nextflow/filter/delimit_counts/nextflow.config
+++ b/target/_private/nextflow/filter/delimit_counts/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/delimit_counts'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Turns an .obs column containing count values into a boolean column based on thresholds.\n'
   author = 'Dorien Roosen'
 }
diff --git a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml
index 24cb4720..484f5d90 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml
+++ b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_mudata_obs_to_tiledb"
 namespace: "tiledb"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -243,7 +243,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -288,11 +288,11 @@ build_info:
   output: "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb"
   executable: "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -322,7 +322,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf
index cd9f554f..85daad83 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf
+++ b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf
@@ -1,4 +1,4 @@
-// move_mudata_obs_to_tiledb v4.0.0
+// move_mudata_obs_to_tiledb v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "move_mudata_obs_to_tiledb",
   "namespace" : "tiledb",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3333,7 +3333,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3393,12 +3393,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3423,7 +3423,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4012,7 +4012,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/tiledb/move_mudata_obs_to_tiledb",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config
index c1eb3213..4a57f077 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config
+++ b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'tiledb/move_mudata_obs_to_tiledb'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Move .obs columns from a MuData modality to an existing tileDB database.\nThe .obs keys should not exist in the database yet; and the observations from the modality and \ntheir order should match with what is already present the tiledb database.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml
index 08b48f0f..e3b3e823 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml
+++ b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_mudata_obsm_to_tiledb"
 namespace: "tiledb"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -220,7 +220,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -265,11 +265,11 @@ build_info:
   output: "target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb"
   executable: "target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -299,7 +299,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf
index ab88a3b7..e8f53850 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf
+++ b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf
@@ -1,4 +1,4 @@
-// move_mudata_obsm_to_tiledb v4.0.0
+// move_mudata_obsm_to_tiledb v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "move_mudata_obsm_to_tiledb",
   "namespace" : "tiledb",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3307,7 +3307,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3367,12 +3367,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3397,7 +3397,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3977,7 +3977,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/tiledb/move_mudata_obsm_to_tiledb",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config
index 192c2ba6..01b1b7a4 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config
+++ b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'tiledb/move_mudata_obsm_to_tiledb'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Move .obsm items from a MuData modality to an existing tileDB database.\nThe .obsm keys should not exist in the database yet; and the observations from the modality and \ntheir order should match with what is already present the tiledb database.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml
index 3d10bf1e..dc8ce008 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml
+++ b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_mudata_obsp_to_tiledb"
 namespace: "tiledb"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -220,7 +220,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -265,11 +265,11 @@ build_info:
   output: "target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb"
   executable: "target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -299,7 +299,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf
index 3ef8a54b..2d6a0b7e 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf
+++ b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf
@@ -1,4 +1,4 @@
-// move_mudata_obsp_to_tiledb v4.0.0
+// move_mudata_obsp_to_tiledb v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "move_mudata_obsp_to_tiledb",
   "namespace" : "tiledb",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3307,7 +3307,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3367,12 +3367,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3397,7 +3397,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3965,7 +3965,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/tiledb/move_mudata_obsp_to_tiledb",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config
index decbb0a9..9f5cdc01 100644
--- a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config
+++ b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'tiledb/move_mudata_obsp_to_tiledb'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Move .obsp items from a MuData modality to an existing tileDB database.\nThe .obsp keys should not exist in the database yet; and the observations from the modality and \ntheir order should match with what is already present the tiledb database.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml b/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml
index 9efcb36f..86196302 100644
--- a/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml
+++ b/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_h5mu"
 namespace: "workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -212,13 +212,13 @@ build_info:
   output: "target/_private/nextflow/workflows/multiomics/split_h5mu"
   executable: "target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/dataflow/split_h5mu"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf b/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf
index fe1b593a..e431128f 100644
--- a/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf
+++ b/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf
@@ -1,4 +1,4 @@
-// split_h5mu v4.0.0
+// split_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_h5mu",
   "namespace" : "workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3305,12 +3305,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/_private/nextflow/workflows/multiomics/split_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3335,7 +3335,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config b/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config
index c9727419..7b86fe22 100644
--- a/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config
+++ b/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/split_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. '
   author = 'Dries Schaumont'
 }
diff --git a/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml b/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml
index 941b02e9..343a3c0e 100644
--- a/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml
+++ b/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_modalities"
 namespace: "workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -183,13 +183,13 @@ build_info:
   output: "target/_private/nextflow/workflows/multiomics/split_modalities"
   executable: "target/_private/nextflow/workflows/multiomics/split_modalities/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/dataflow/split_modalities"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -219,7 +219,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf b/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf
index 2bd887c9..01abda2b 100644
--- a/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf
+++ b/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf
@@ -1,4 +1,4 @@
-// split_modalities v4.0.0
+// split_modalities v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_modalities",
   "namespace" : "workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3274,12 +3274,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/_private/nextflow/workflows/multiomics/split_modalities",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3304,7 +3304,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config b/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config
index 990d7f4c..24eb55e1 100644
--- a/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config
+++ b/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/split_modalities'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'A pipeline to split a multimodal mudata files into several unimodal mudata files.'
   author = 'Dries Schaumont'
 }
diff --git a/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml b/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml
index 595ba1f9..2c4d3598 100644
--- a/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml
+++ b/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "log_normalize"
 namespace: "workflows/rna"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -198,7 +198,7 @@ build_info:
   output: "target/_private/nextflow/workflows/rna/log_normalize"
   executable: "target/_private/nextflow/workflows/rna/log_normalize/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/transform/normalize_total"
@@ -206,7 +206,7 @@ build_info:
   - "target/nextflow/transform/delete_layer"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -236,7 +236,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_private/nextflow/workflows/rna/log_normalize/main.nf b/target/_private/nextflow/workflows/rna/log_normalize/main.nf
index 6b15a043..b2355135 100644
--- a/target/_private/nextflow/workflows/rna/log_normalize/main.nf
+++ b/target/_private/nextflow/workflows/rna/log_normalize/main.nf
@@ -1,4 +1,4 @@
-// log_normalize v4.0.0
+// log_normalize v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "log_normalize",
   "namespace" : "workflows/rna",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3294,12 +3294,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/_private/nextflow/workflows/rna/log_normalize",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3324,7 +3324,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config b/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config
index 813fc412..b8d823cb 100644
--- a/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config
+++ b/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/rna/log_normalize'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs normalization and subsequent log-transformation of raw count data.'
   author = 'Dries Schaumont'
 }
diff --git a/target/_test/executable/download/sync_test_resources/.config.vsh.yaml b/target/_test/executable/download/sync_test_resources/.config.vsh.yaml
index 636cd20a..eabb62bb 100644
--- a/target/_test/executable/download/sync_test_resources/.config.vsh.yaml
+++ b/target/_test/executable/download/sync_test_resources/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "sync_test_resources"
 namespace: "download"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -174,7 +174,7 @@ engines:
   id: "docker"
   image: "amazon/aws-cli:2.17.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "yum"
@@ -195,11 +195,11 @@ build_info:
   output: "target/_test/executable/download/sync_test_resources"
   executable: "target/_test/executable/download/sync_test_resources/sync_test_resources"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -229,7 +229,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/download/sync_test_resources/sync_test_resources b/target/_test/executable/download/sync_test_resources/sync_test_resources
index 904fe07e..86aa3ffa 100755
--- a/target/_test/executable/download/sync_test_resources/sync_test_resources
+++ b/target/_test/executable/download/sync_test_resources/sync_test_resources
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# sync_test_resources v4.0.0
+# sync_test_resources v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component download sync_test_resources"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "sync_test_resources v4.0.0"
+  echo "sync_test_resources v4.0.1"
   echo ""
   echo "Sync test resources to the local filesystem"
   echo ""
@@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "sync_test_resources v4.0.0"
+            echo "sync_test_resources v4.0.1"
             exit
             ;;
         --input)
@@ -821,7 +821,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/sync_test_resources:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/sync_test_resources:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml
index 00a3b691..9ed8015f 100644
--- a/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "celltypist_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -131,7 +131,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,11 +164,11 @@ build_info:
   output: "target/_test/executable/test_workflows/annotation/celltypist_test"
   executable: "target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -198,7 +198,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test b/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test
index 4a173ceb..db25f6c0 100755
--- a/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test
+++ b/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# celltypist_test v4.0.0
+# celltypist_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation celltypist_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:43Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "celltypist_test v4.0.0"
+  echo "celltypist_test v4.0.1"
   echo ""
   echo "This component tests the output of the annotation of the celltypist workflow."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "celltypist_test v4.0.0"
+            echo "celltypist_test v4.0.1"
             exit
             ;;
         --input)
@@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/celltypist_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/celltypist_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml
index 13ebe31f..7c7ac57d 100644
--- a/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "harmony_knn_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/executable/test_workflows/annotation/harmony_knn_test"
   executable: "target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test b/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test
index 44239e1f..34af522b 100755
--- a/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test
+++ b/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# harmony_knn_test v4.0.0
+# harmony_knn_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation harmony_knn_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:43Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "harmony_knn_test v4.0.0"
+  echo "harmony_knn_test v4.0.1"
   echo ""
   echo "This component tests the output of the annotation of the harmony_knn of"
   echo "workflow."
@@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "harmony_knn_test v4.0.0"
+            echo "harmony_knn_test v4.0.1"
             exit
             ;;
         --input)
@@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/harmony_knn_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/harmony_knn_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml
index 3de5541b..6b1fc245 100644
--- a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanvi_scarches_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/executable/test_workflows/annotation/scanvi_scarches_test"
   executable: "target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test
index 86f84ad5..6ae3a63c 100755
--- a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test
+++ b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scanvi_scarches_test v4.0.0
+# scanvi_scarches_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation scanvi_scarches_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scanvi_scarches_test v4.0.0"
+  echo "scanvi_scarches_test v4.0.1"
   echo ""
   echo "This component tests the output of the annotation of the scanvi annotation"
   echo "workflow."
@@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scanvi_scarches_test v4.0.0"
+            echo "scanvi_scarches_test v4.0.1"
             exit
             ;;
         --input)
@@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scanvi_scarches_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scanvi_scarches_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml
index 4e276ee2..e6cc3209 100644
--- a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scgpt_annotation_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -129,7 +129,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -162,11 +162,11 @@ build_info:
   output: "target/_test/executable/test_workflows/annotation/scgpt_annotation_test"
   executable: "target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -196,7 +196,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test
index ea774c59..e0ce72c6 100755
--- a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test
+++ b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scgpt_annotation_test v4.0.0
+# scgpt_annotation_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation scgpt_annotation_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:43Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scgpt_annotation_test v4.0.0"
+  echo "scgpt_annotation_test v4.0.1"
   echo ""
   echo "This component test the output of the the scgpt_annotation workflow."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scgpt_annotation_test v4.0.0"
+            echo "scgpt_annotation_test v4.0.1"
             exit
             ;;
         --input)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scgpt_annotation_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scgpt_annotation_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml
index 991b036a..056e827c 100644
--- a/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvi_knn_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/executable/test_workflows/annotation/scvi_knn_test"
   executable: "target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test b/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test
index 2e29880b..6dfecd9a 100755
--- a/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test
+++ b/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scvi_knn_test v4.0.0
+# scvi_knn_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation scvi_knn_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:43Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scvi_knn_test v4.0.0"
+  echo "scvi_knn_test v4.0.1"
   echo ""
   echo "This component tests the output of the annotation of the scvi_knn of workflow."
   echo ""
@@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scvi_knn_test v4.0.0"
+            echo "scvi_knn_test v4.0.1"
             exit
             ;;
         --input)
@@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scvi_knn_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scvi_knn_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml
index 51de561d..3a60d214 100644
--- a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "pseudobulk_deseq2_test"
 namespace: "test_workflows/differential_expression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -118,7 +118,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -151,11 +151,11 @@ build_info:
   output: "target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test"
   executable: "target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -185,7 +185,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test
index 5de1d029..b5eb8144 100755
--- a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test
+++ b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# pseudobulk_deseq2_test v4.0.0
+# pseudobulk_deseq2_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/differential_expression pseudobulk_deseq2_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:42Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "pseudobulk_deseq2_test v4.0.0"
+  echo "pseudobulk_deseq2_test v4.0.1"
   echo ""
   echo "This component tests the output of the pseudobulk_deseq2 differential expression"
   echo "analysis workflow."
@@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "pseudobulk_deseq2_test v4.0.0"
+            echo "pseudobulk_deseq2_test v4.0.1"
             exit
             ;;
         --input)
@@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/differential_expression/pseudobulk_deseq2_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/differential_expression/pseudobulk_deseq2_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml
index 0fdfc65f..5b1e4d29 100644
--- a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bd_rhapsody_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/executable/test_workflows/ingestion/bd_rhapsody_test"
   executable: "target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test
index 3b6e4d87..52598709 100755
--- a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test
+++ b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# bd_rhapsody_test v4.0.0
+# bd_rhapsody_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion bd_rhapsody_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:26Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bd_rhapsody_test v4.0.0"
+  echo "bd_rhapsody_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of the bd_rhapsody"
   echo "workflow."
@@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "bd_rhapsody_test v4.0.0"
+            echo "bd_rhapsody_test v4.0.1"
             exit
             ;;
         --input)
@@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/bd_rhapsody_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/bd_rhapsody_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml
index 53b4c597..d62b4134 100644
--- a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_mapping_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/executable/test_workflows/ingestion/cellranger_mapping_test"
   executable: "target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test
index 9135480a..d0aebe33 100755
--- a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test
+++ b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_mapping_test v4.0.0
+# cellranger_mapping_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion cellranger_mapping_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:25Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_mapping_test v4.0.0"
+  echo "cellranger_mapping_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of the cellranger mapping"
   echo "workflow."
@@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_mapping_test v4.0.0"
+            echo "cellranger_mapping_test v4.0.1"
             exit
             ;;
         --input)
@@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_mapping_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_mapping_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml
index 32e0e705..7cef69c0 100644
--- a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_multi_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/executable/test_workflows/ingestion/cellranger_multi_test"
   executable: "target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test
index 94382776..fc9c0af5 100755
--- a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test
+++ b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_multi_test v4.0.0
+# cellranger_multi_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion cellranger_multi_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:24Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_multi_test v4.0.0"
+  echo "cellranger_multi_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of the cellranger multi"
   echo "workflow."
@@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_multi_test v4.0.0"
+            echo "cellranger_multi_test v4.0.1"
             exit
             ;;
         --input)
@@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_multi_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_multi_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml
index 799ea5d4..a11859fb 100644
--- a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_postprocessing_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -140,7 +140,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -173,11 +173,11 @@ build_info:
   output: "target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test"
   executable: "target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -207,7 +207,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test
index 6fc76e3b..6958c538 100755
--- a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test
+++ b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_postprocessing_test v4.0.0
+# cellranger_postprocessing_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion cellranger_postprocessing_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:25Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_postprocessing_test v4.0.0"
+  echo "cellranger_postprocessing_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of the cellranger"
   echo "postprocessing workflow."
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_postprocessing_test v4.0.0"
+            echo "cellranger_postprocessing_test v4.0.1"
             exit
             ;;
         --input)
@@ -770,7 +770,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_postprocessing_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_postprocessing_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml
index de714ae4..ed25fab2 100644
--- a/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "conversion_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/executable/test_workflows/ingestion/conversion_test"
   executable: "target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test b/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test
index 3572e888..8c4d0e93 100755
--- a/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test
+++ b/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# conversion_test v4.0.0
+# conversion_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion conversion_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:25Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "conversion_test v4.0.0"
+  echo "conversion_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of the conversion"
   echo "workflow."
@@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "conversion_test v4.0.0"
+            echo "conversion_test v4.0.1"
             exit
             ;;
         --input)
@@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/conversion_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/conversion_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml
index 603373ee..12e73c80 100644
--- a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi_leiden_test"
 namespace: "test_workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -163,11 +163,11 @@ build_info:
   output: "target/_test/executable/test_workflows/integration/totalvi_leiden_test"
   executable: "target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -197,7 +197,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test
index 85cfbdae..129584d0 100755
--- a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test
+++ b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# totalvi_leiden_test v4.0.0
+# totalvi_leiden_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/integration totalvi_leiden_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:42Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:29Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "totalvi_leiden_test v4.0.0"
+  echo "totalvi_leiden_test v4.0.1"
   echo ""
   echo "This component tests the output of totalvi_leiden integration workflow."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "totalvi_leiden_test v4.0.0"
+            echo "totalvi_leiden_test v4.0.1"
             exit
             ;;
         --input)
@@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/integration/totalvi_leiden_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/integration/totalvi_leiden_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml
index 5b4ffe48..4b02e6fe 100644
--- a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "dimensionality_reduction_test"
 namespace: "test_workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -150,11 +150,11 @@ build_info:
   output: "target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test"
   executable: "target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -184,7 +184,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test
index 1494f525..11042219 100755
--- a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test
+++ b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# dimensionality_reduction_test v4.0.0
+# dimensionality_reduction_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics dimensionality_reduction_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:45Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "dimensionality_reduction_test v4.0.0"
+  echo "dimensionality_reduction_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of"
   echo "dimensionality_reduction."
@@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "dimensionality_reduction_test v4.0.0"
+            echo "dimensionality_reduction_test v4.0.1"
             exit
             ;;
         --input)
@@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/dimensionality_reduction_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/dimensionality_reduction_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml
index 873d379a..8a54f490 100644
--- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "workflow_test"
 namespace: "test_workflows/multiomics/process_batches"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -136,7 +136,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -169,11 +169,11 @@ build_info:
   output: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test"
   executable: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -203,7 +203,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test
index aa8b6416..2e95a9c7 100755
--- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test
+++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# workflow_test v4.0.0
+# workflow_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics/process_batches workflow_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:45Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "workflow_test v4.0.0"
+  echo "workflow_test v4.0.1"
   echo ""
   echo "This component tests the output of the integration test of process_batches"
   echo "test_wf."
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "workflow_test v4.0.0"
+            echo "workflow_test v4.0.1"
             exit
             ;;
         --input)
@@ -755,7 +755,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml
index e0b2e17c..60fa90c6 100644
--- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "workflow_test2"
 namespace: "test_workflows/multiomics/process_batches"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -136,7 +136,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -169,11 +169,11 @@ build_info:
   output: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2"
   executable: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -203,7 +203,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2 b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2
index 0973c3ca..6c3ff0ac 100755
--- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2
+++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# workflow_test2 v4.0.0
+# workflow_test2 v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics/process_batches workflow_test2"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "workflow_test2 v4.0.0"
+  echo "workflow_test2 v4.0.1"
   echo ""
   echo "This component tests the output of the integration test of process_batches"
   echo "test_wf2."
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "workflow_test2 v4.0.0"
+            echo "workflow_test2 v4.0.1"
             exit
             ;;
         --input)
@@ -755,7 +755,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test2:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test2:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml
index 8d6525db..45d28828 100644
--- a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_h5mu_test"
 namespace: "test_workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -145,7 +145,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -178,11 +178,11 @@ build_info:
   output: "target/_test/executable/test_workflows/multiomics/split_h5mu_test"
   executable: "target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -212,7 +212,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test
index ac36983a..c0c934df 100755
--- a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test
+++ b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# split_h5mu_test v4.0.0
+# split_h5mu_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics split_h5mu_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "split_h5mu_test v4.0.0"
+  echo "split_h5mu_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of split_h5mu."
   echo ""
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "split_h5mu_test v4.0.0"
+            echo "split_h5mu_test v4.0.1"
             exit
             ;;
         --input)
@@ -770,7 +770,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_h5mu_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_h5mu_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml
index 70f8deea..7500dd8b 100644
--- a/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_modalities_test"
 namespace: "test_workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -145,7 +145,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -178,11 +178,11 @@ build_info:
   output: "target/_test/executable/test_workflows/multiomics/split_modalities_test"
   executable: "target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -212,7 +212,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test b/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test
index 3221e309..02d7d64b 100755
--- a/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test
+++ b/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# split_modalities_test v4.0.0
+# split_modalities_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics split_modalities_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:45Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "split_modalities_test v4.0.0"
+  echo "split_modalities_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of split_modalities."
   echo ""
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "split_modalities_test v4.0.0"
+            echo "split_modalities_test v4.0.1"
             exit
             ;;
         --input)
@@ -770,7 +770,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_modalities_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_modalities_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml b/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml
index a3548d6f..5c040cd2 100644
--- a/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml
+++ b/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "qc_test"
 namespace: "test_workflows/qc"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -134,7 +134,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -167,11 +167,11 @@ build_info:
   output: "target/_test/executable/test_workflows/qc/qc_test"
   executable: "target/_test/executable/test_workflows/qc/qc_test/qc_test"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -201,7 +201,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/executable/test_workflows/qc/qc_test/qc_test b/target/_test/executable/test_workflows/qc/qc_test/qc_test
index 4ae00ac7..a71b5fab 100755
--- a/target/_test/executable/test_workflows/qc/qc_test/qc_test
+++ b/target/_test/executable/test_workflows/qc/qc_test/qc_test
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# qc_test v4.0.0
+# qc_test v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/qc qc_test"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:42Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "qc_test v4.0.0"
+  echo "qc_test v4.0.1"
   echo ""
   echo "This component test the output of the integration test of the QC workflow."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "qc_test v4.0.0"
+            echo "qc_test v4.0.1"
             exit
             ;;
         --input)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/qc/qc_test:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/qc/qc_test:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml b/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml
index 536d7f0c..35da87a4 100644
--- a/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml
+++ b/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "sync_test_resources"
 namespace: "download"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -174,7 +174,7 @@ engines:
   id: "docker"
   image: "amazon/aws-cli:2.17.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "yum"
@@ -195,11 +195,11 @@ build_info:
   output: "target/_test/nextflow/download/sync_test_resources"
   executable: "target/_test/nextflow/download/sync_test_resources/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -229,7 +229,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/download/sync_test_resources/main.nf b/target/_test/nextflow/download/sync_test_resources/main.nf
index 3e539d68..7cd074f3 100644
--- a/target/_test/nextflow/download/sync_test_resources/main.nf
+++ b/target/_test/nextflow/download/sync_test_resources/main.nf
@@ -1,4 +1,4 @@
-// sync_test_resources v4.0.0
+// sync_test_resources v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "sync_test_resources",
   "namespace" : "download",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3257,7 +3257,7 @@ meta = [
       "id" : "docker",
       "image" : "amazon/aws-cli:2.17.11",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3285,12 +3285,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/download/sync_test_resources",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3315,7 +3315,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3801,7 +3801,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/download/sync_test_resources",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/download/sync_test_resources/nextflow.config b/target/_test/nextflow/download/sync_test_resources/nextflow.config
index 99030537..388ec6af 100644
--- a/target/_test/nextflow/download/sync_test_resources/nextflow.config
+++ b/target/_test/nextflow/download/sync_test_resources/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'download/sync_test_resources'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Sync test resources to the local filesystem'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml
index fe033997..0024264c 100644
--- a/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "celltypist_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -131,7 +131,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,11 +164,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/annotation/celltypist_test"
   executable: "target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -198,7 +198,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf b/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf
index 6f9f6d47..f37bf457 100644
--- a/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf
+++ b/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf
@@ -1,4 +1,4 @@
-// celltypist_test v4.0.0
+// celltypist_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "celltypist_test",
   "namespace" : "test_workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3200,7 +3200,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3241,12 +3241,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/celltypist_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3271,7 +3271,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3746,7 +3746,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/annotation/celltypist_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config
index 0aec5880..fc2a1851 100644
--- a/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/annotation/celltypist_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the annotation of the celltypist workflow.'
   author = 'Dorien Roosen'
 }
diff --git a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml
index 626b2ddb..4429df59 100644
--- a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "harmony_knn_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/annotation/harmony_knn_test"
   executable: "target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf
index 7e08a6ca..8b81d949 100644
--- a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf
+++ b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf
@@ -1,4 +1,4 @@
-// harmony_knn_test v4.0.0
+// harmony_knn_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "harmony_knn_test",
   "namespace" : "test_workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3187,7 +3187,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3228,12 +3228,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/harmony_knn_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3258,7 +3258,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3741,7 +3741,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/annotation/harmony_knn_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config
index 1a6c79cc..85f1ba9d 100644
--- a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/annotation/harmony_knn_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the annotation of the harmony_knn of workflow.'
   author = 'Dorien Roosen'
 }
diff --git a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml
index 67faa849..3bc4f91c 100644
--- a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanvi_scarches_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test"
   executable: "target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf
index e89f872c..cf07c809 100644
--- a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf
+++ b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf
@@ -1,4 +1,4 @@
-// scanvi_scarches_test v4.0.0
+// scanvi_scarches_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scanvi_scarches_test",
   "namespace" : "test_workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3187,7 +3187,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3228,12 +3228,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3258,7 +3258,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3737,7 +3737,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/annotation/scanvi_scarches_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config
index beb57534..dc37f12e 100644
--- a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/annotation/scanvi_scarches_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the annotation of the scanvi annotation workflow.'
   author = 'Dorien Roosen'
 }
diff --git a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml
index f8f803d4..a54e5df9 100644
--- a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scgpt_annotation_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -129,7 +129,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -162,11 +162,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test"
   executable: "target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -196,7 +196,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf
index 76ffe0ea..79746256 100644
--- a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf
+++ b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf
@@ -1,4 +1,4 @@
-// scgpt_annotation_test v4.0.0
+// scgpt_annotation_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scgpt_annotation_test",
   "namespace" : "test_workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3199,7 +3199,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3240,12 +3240,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3270,7 +3270,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3751,7 +3751,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/annotation/scgpt_annotation_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config
index 98e3f709..59ba13c5 100644
--- a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/annotation/scgpt_annotation_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the the scgpt_annotation workflow.'
   author = 'Dorien Roosen'
 }
diff --git a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml
index 83a8b342..8c526b62 100644
--- a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvi_knn_test"
 namespace: "test_workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/annotation/scvi_knn_test"
   executable: "target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf
index 607383dd..88aa8b60 100644
--- a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf
+++ b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf
@@ -1,4 +1,4 @@
-// scvi_knn_test v4.0.0
+// scvi_knn_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scvi_knn_test",
   "namespace" : "test_workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3187,7 +3187,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3228,12 +3228,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/scvi_knn_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3258,7 +3258,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3738,7 +3738,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/annotation/scvi_knn_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config
index ec2af129..8463b75d 100644
--- a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/annotation/scvi_knn_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the annotation of the scvi_knn of workflow.'
   author = 'Dorien Roosen'
 }
diff --git a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml
index 87e3553f..a5af9560 100644
--- a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "pseudobulk_deseq2_test"
 namespace: "test_workflows/differential_expression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -118,7 +118,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -151,11 +151,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test"
   executable: "target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -185,7 +185,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf
index adb73623..8bdb74bf 100644
--- a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf
+++ b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf
@@ -1,4 +1,4 @@
-// pseudobulk_deseq2_test v4.0.0
+// pseudobulk_deseq2_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "pseudobulk_deseq2_test",
   "namespace" : "test_workflows/differential_expression",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3183,7 +3183,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3224,12 +3224,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3254,7 +3254,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3750,7 +3750,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/differential_expression/pseudobulk_deseq2_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config
index 0d1eb3d5..e4b3208b 100644
--- a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/differential_expression/pseudobulk_deseq2_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the pseudobulk_deseq2 differential expression analysis workflow.'
   author = 'Dorien Roosen'
 }
diff --git a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml
index d3b12045..4be11b7c 100644
--- a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bd_rhapsody_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test"
   executable: "target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf
index d6eead22..e4a5a51b 100644
--- a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf
+++ b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf
@@ -1,4 +1,4 @@
-// bd_rhapsody_test v4.0.0
+// bd_rhapsody_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bd_rhapsody_test",
   "namespace" : "test_workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3187,7 +3187,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3228,12 +3228,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3258,7 +3258,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3743,7 +3743,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/ingestion/bd_rhapsody_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config
index a9dee564..99b72c38 100644
--- a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/ingestion/bd_rhapsody_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of the bd_rhapsody workflow.'
   author = 'Jakub Majercik'
 }
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml
index 849b9c9d..3faf2103 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_mapping_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test"
   executable: "target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf
index 58ffaae6..0ef8a88c 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf
@@ -1,4 +1,4 @@
-// cellranger_mapping_test v4.0.0
+// cellranger_mapping_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_mapping_test",
   "namespace" : "test_workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3187,7 +3187,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3228,12 +3228,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3258,7 +3258,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3721,7 +3721,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/ingestion/cellranger_mapping_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config
index 1f65d61a..3c66a1e8 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/ingestion/cellranger_mapping_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of the cellranger mapping workflow.'
   author = 'Jakub Majercik'
 }
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml
index 18998e0f..c0874ca3 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_multi_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test"
   executable: "target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf
index 8e75dbd3..a3c790e2 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf
@@ -1,4 +1,4 @@
-// cellranger_multi_test v4.0.0
+// cellranger_multi_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_multi_test",
   "namespace" : "test_workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3187,7 +3187,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3228,12 +3228,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3258,7 +3258,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3725,7 +3725,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/ingestion/cellranger_multi_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config
index 3c3908b8..9c1154a0 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/ingestion/cellranger_multi_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of the cellranger multi workflow.'
   author = 'Jakub Majercik'
 }
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml
index 205507df..49c37683 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_postprocessing_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -140,7 +140,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -173,11 +173,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test"
   executable: "target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -207,7 +207,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf
index ed5f8456..aa9be608 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf
@@ -1,4 +1,4 @@
-// cellranger_postprocessing_test v4.0.0
+// cellranger_postprocessing_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_postprocessing_test",
   "namespace" : "test_workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3210,7 +3210,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3251,12 +3251,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3281,7 +3281,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3756,7 +3756,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/ingestion/cellranger_postprocessing_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config
index 8a9d0d39..9cc7771f 100644
--- a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/ingestion/cellranger_postprocessing_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of the cellranger postprocessing workflow.'
   author = 'Jakub Majercik'
 }
diff --git a/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml
index 7f26526d..aba1044e 100644
--- a/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "conversion_test"
 namespace: "test_workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -120,7 +120,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -153,11 +153,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/ingestion/conversion_test"
   executable: "target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -187,7 +187,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf
index 5e406de1..32555d11 100644
--- a/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf
+++ b/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf
@@ -1,4 +1,4 @@
-// conversion_test v4.0.0
+// conversion_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "conversion_test",
   "namespace" : "test_workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3187,7 +3187,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3228,12 +3228,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/conversion_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3258,7 +3258,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3715,7 +3715,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/ingestion/conversion_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config
index 6f9b32bc..2a32461d 100644
--- a/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/ingestion/conversion_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of the conversion workflow.'
   author = 'Jakub Majercik'
 }
diff --git a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml
index 469b58af..fcfbeda6 100644
--- a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi_leiden_test"
 namespace: "test_workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   info:
@@ -130,7 +130,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -163,11 +163,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/integration/totalvi_leiden_test"
   executable: "target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -197,7 +197,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf
index ee01c39d..ee1de4be 100644
--- a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf
+++ b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf
@@ -1,4 +1,4 @@
-// totalvi_leiden_test v4.0.0
+// totalvi_leiden_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "totalvi_leiden_test",
   "namespace" : "test_workflows/integration",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3200,7 +3200,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3241,12 +3241,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3271,7 +3271,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3751,7 +3751,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/integration/totalvi_leiden_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config
index 22ab0cdb..a1371e21 100644
--- a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/integration/totalvi_leiden_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of totalvi_leiden integration workflow.'
   author = 'Dorien Roosen'
 }
diff --git a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml
index 5f6b1b74..be54b8cc 100644
--- a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "dimensionality_reduction_test"
 namespace: "test_workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -150,11 +150,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test"
   executable: "target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -184,7 +184,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf
index 6408c5ef..b5bb977e 100644
--- a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf
+++ b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf
@@ -1,4 +1,4 @@
-// dimensionality_reduction_test v4.0.0
+// dimensionality_reduction_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "dimensionality_reduction_test",
   "namespace" : "test_workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Kai Waldrant",
@@ -3189,7 +3189,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3225,12 +3225,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3255,7 +3255,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3710,7 +3710,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/multiomics/dimensionality_reduction_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config
index c12c038f..615f9736 100644
--- a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/multiomics/dimensionality_reduction_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of dimensionality_reduction.'
   author = 'Kai Waldrant'
 }
diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml
index d8ff019e..fa634a56 100644
--- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "workflow_test"
 namespace: "test_workflows/multiomics/process_batches"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -136,7 +136,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -169,11 +169,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test"
   executable: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -203,7 +203,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf
index 4eb6f905..8e657edd 100644
--- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf
+++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf
@@ -1,4 +1,4 @@
-// workflow_test v4.0.0
+// workflow_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "workflow_test",
   "namespace" : "test_workflows/multiomics/process_batches",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Kai Waldrant",
@@ -3206,7 +3206,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3247,12 +3247,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3277,7 +3277,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3744,7 +3744,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem"
diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config
index 430f4635..99784c43 100644
--- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/multiomics/process_batches/workflow_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the integration test of process_batches test_wf.'
   author = 'Kai Waldrant'
 }
diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml
index 74bb58dc..655e817e 100644
--- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "workflow_test2"
 namespace: "test_workflows/multiomics/process_batches"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -136,7 +136,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -169,11 +169,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2"
   executable: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -203,7 +203,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf
index 7604fd96..c4596863 100644
--- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf
+++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf
@@ -1,4 +1,4 @@
-// workflow_test2 v4.0.0
+// workflow_test2 v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "workflow_test2",
   "namespace" : "test_workflows/multiomics/process_batches",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Kai Waldrant",
@@ -3206,7 +3206,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3247,12 +3247,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3277,7 +3277,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3769,7 +3769,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test2",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem"
diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config
index f9112209..afd395ce 100644
--- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config
+++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/multiomics/process_batches/workflow_test2'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the integration test of process_batches test_wf2.'
   author = 'Kai Waldrant'
 }
diff --git a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml
index 469855b0..a627ae72 100644
--- a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_h5mu_test"
 namespace: "test_workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -145,7 +145,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -178,11 +178,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/multiomics/split_h5mu_test"
   executable: "target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -212,7 +212,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf
index 7ff528a0..0c1e436f 100644
--- a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf
+++ b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf
@@ -1,4 +1,4 @@
-// split_h5mu_test v4.0.0
+// split_h5mu_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_h5mu_test",
   "namespace" : "test_workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Kai Waldrant",
@@ -3217,7 +3217,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3258,12 +3258,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3288,7 +3288,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3776,7 +3776,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/multiomics/split_h5mu_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config
index e5895d80..57f7045a 100644
--- a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/multiomics/split_h5mu_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of split_h5mu.'
   author = 'Kai Waldrant'
 }
diff --git a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml
index 74bd8cfb..55f7b46b 100644
--- a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_modalities_test"
 namespace: "test_workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Kai Waldrant"
   info:
@@ -145,7 +145,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -178,11 +178,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/multiomics/split_modalities_test"
   executable: "target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -212,7 +212,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf
index 2eb9d12e..561c34b6 100644
--- a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf
+++ b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf
@@ -1,4 +1,4 @@
-// split_modalities_test v4.0.0
+// split_modalities_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_modalities_test",
   "namespace" : "test_workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Kai Waldrant",
@@ -3217,7 +3217,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3258,12 +3258,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/split_modalities_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3288,7 +3288,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3778,7 +3778,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/multiomics/split_modalities_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config
index c1b79f17..ee63cc75 100644
--- a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/multiomics/split_modalities_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of split_modalities.'
   author = 'Kai Waldrant'
 }
diff --git a/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml
index d0759c95..ab5e78c2 100644
--- a/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml
+++ b/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "qc_test"
 namespace: "test_workflows/qc"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   info:
@@ -134,7 +134,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -167,11 +167,11 @@ build_info:
   output: "target/_test/nextflow/test_workflows/qc/qc_test"
   executable: "target/_test/nextflow/test_workflows/qc/qc_test/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -201,7 +201,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/_test/nextflow/test_workflows/qc/qc_test/main.nf b/target/_test/nextflow/test_workflows/qc/qc_test/main.nf
index 7d5c0050..4158b5a8 100644
--- a/target/_test/nextflow/test_workflows/qc/qc_test/main.nf
+++ b/target/_test/nextflow/test_workflows/qc/qc_test/main.nf
@@ -1,4 +1,4 @@
-// qc_test v4.0.0
+// qc_test v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "qc_test",
   "namespace" : "test_workflows/qc",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3205,7 +3205,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3246,12 +3246,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/qc/qc_test",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3276,7 +3276,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3785,7 +3785,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/qc/qc_test",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config b/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config
index 0e691196..171f7a58 100644
--- a/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config
+++ b/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/qc/qc_test'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component test the output of the integration test of the QC workflow.'
   author = 'Jakub Majercik'
 }
diff --git a/target/executable/annotate/celltypist/.config.vsh.yaml b/target/executable/annotate/celltypist/.config.vsh.yaml
index 71257470..c741a7aa 100644
--- a/target/executable/annotate/celltypist/.config.vsh.yaml
+++ b/target/executable/annotate/celltypist/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "celltypist"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -384,7 +384,7 @@ engines:
   id: "docker"
   image: "nvcr.io/nvidia/pytorch:25.11-py3"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -431,11 +431,11 @@ build_info:
   output: "target/executable/annotate/celltypist"
   executable: "target/executable/annotate/celltypist/celltypist"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -465,7 +465,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/annotate/celltypist/celltypist b/target/executable/annotate/celltypist/celltypist
index fb8e80ad..53549cd4 100755
--- a/target/executable/annotate/celltypist/celltypist
+++ b/target/executable/annotate/celltypist/celltypist
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# celltypist v4.0.0
+# celltypist v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component annotate celltypist"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "celltypist v4.0.0"
+  echo "celltypist v4.0.1"
   echo ""
   echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of"
   echo "logistic regression classifiers optimised by the stochastic gradient descent"
@@ -769,7 +769,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "celltypist v4.0.0"
+            echo "celltypist v4.0.1"
             exit
             ;;
         --input)
@@ -1102,7 +1102,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/celltypist:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/celltypist:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/annotate/onclass/.config.vsh.yaml b/target/executable/annotate/onclass/.config.vsh.yaml
index 1d8a4ce4..0744b49f 100644
--- a/target/executable/annotate/onclass/.config.vsh.yaml
+++ b/target/executable/annotate/onclass/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "onclass"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -365,7 +365,7 @@ engines:
   id: "docker"
   image: "python:3.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -405,11 +405,11 @@ build_info:
   output: "target/executable/annotate/onclass"
   executable: "target/executable/annotate/onclass/onclass"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -439,7 +439,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/annotate/onclass/onclass b/target/executable/annotate/onclass/onclass
index 92369853..839574ba 100755
--- a/target/executable/annotate/onclass/onclass
+++ b/target/executable/annotate/onclass/onclass
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# onclass v4.0.0
+# onclass v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component annotate onclass"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:38Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "onclass v4.0.0"
+  echo "onclass v4.0.1"
   echo ""
   echo "OnClass is a python package for single-cell cell type annotation. It uses the"
   echo "Cell Ontology to capture the cell type similarity."
@@ -758,7 +758,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "onclass v4.0.0"
+            echo "onclass v4.0.1"
             exit
             ;;
         --input)
@@ -1086,7 +1086,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/onclass:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/onclass:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/annotate/popv/.config.vsh.yaml b/target/executable/annotate/popv/.config.vsh.yaml
index 02f6762d..24475ac2 100644
--- a/target/executable/annotate/popv/.config.vsh.yaml
+++ b/target/executable/annotate/popv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "popv"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Matthias Beyens"
   roles:
@@ -310,7 +310,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -361,11 +361,11 @@ build_info:
   output: "target/executable/annotate/popv"
   executable: "target/executable/annotate/popv/popv"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -395,7 +395,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/annotate/popv/popv b/target/executable/annotate/popv/popv
index 5b70fe57..0f83c478 100755
--- a/target/executable/annotate/popv/popv
+++ b/target/executable/annotate/popv/popv
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# popv v4.0.0
+# popv v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -466,10 +466,10 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git
 
 LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component annotate popv"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -586,7 +586,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "popv v4.0.0"
+  echo "popv v4.0.1"
   echo ""
   echo "Performs popular major vote cell typing on single cell sequence data using"
   echo "multiple algorithms. Note that this is a one-shot version of PopV."
@@ -728,7 +728,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "popv v4.0.0"
+            echo "popv v4.0.1"
             exit
             ;;
         --input)
@@ -985,7 +985,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/popv:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/popv:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/annotate/random_forest_annotation/.config.vsh.yaml b/target/executable/annotate/random_forest_annotation/.config.vsh.yaml
index 7187bf4d..0edc3ce7 100644
--- a/target/executable/annotate/random_forest_annotation/.config.vsh.yaml
+++ b/target/executable/annotate/random_forest_annotation/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "random_forest_annotation"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -373,7 +373,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -420,11 +420,11 @@ build_info:
   output: "target/executable/annotate/random_forest_annotation"
   executable: "target/executable/annotate/random_forest_annotation/random_forest_annotation"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -454,7 +454,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/annotate/random_forest_annotation/random_forest_annotation b/target/executable/annotate/random_forest_annotation/random_forest_annotation
index e1121b3f..f972ae38 100755
--- a/target/executable/annotate/random_forest_annotation/random_forest_annotation
+++ b/target/executable/annotate/random_forest_annotation/random_forest_annotation
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# random_forest_annotation v4.0.0
+# random_forest_annotation v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component annotate random_forest_annotation"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "random_forest_annotation v4.0.0"
+  echo "random_forest_annotation v4.0.1"
   echo ""
   echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of"
   echo "random forest."
@@ -770,7 +770,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "random_forest_annotation v4.0.0"
+            echo "random_forest_annotation v4.0.1"
             exit
             ;;
         --input)
@@ -1092,7 +1092,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/random_forest_annotation:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/random_forest_annotation:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/annotate/scanvi/.config.vsh.yaml b/target/executable/annotate/scanvi/.config.vsh.yaml
index ed594dcd..b878af9a 100644
--- a/target/executable/annotate/scanvi/.config.vsh.yaml
+++ b/target/executable/annotate/scanvi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanvi"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -405,7 +405,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -442,11 +442,11 @@ build_info:
   output: "target/executable/annotate/scanvi"
   executable: "target/executable/annotate/scanvi/scanvi"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -476,7 +476,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/annotate/scanvi/scanvi b/target/executable/annotate/scanvi/scanvi
index 42827549..88765d07 100755
--- a/target/executable/annotate/scanvi/scanvi
+++ b/target/executable/annotate/scanvi/scanvi
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scanvi v4.0.0
+# scanvi v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Jakub Majercik, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component annotate scanvi"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scanvi v4.0.0"
+  echo "scanvi v4.0.1"
   echo ""
   echo "scANVI () is a semi-supervised model for single-cell transcriptomics data."
   echo "scANVI is an scVI extension that can leverage the cell type knowledge for a"
@@ -761,7 +761,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scanvi v4.0.0"
+            echo "scanvi v4.0.1"
             exit
             ;;
         --input)
@@ -1117,7 +1117,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/scanvi:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/scanvi:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/annotate/singler/.config.vsh.yaml b/target/executable/annotate/singler/.config.vsh.yaml
index c64e4498..3dde4793 100644
--- a/target/executable/annotate/singler/.config.vsh.yaml
+++ b/target/executable/annotate/singler/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "singler"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -424,7 +424,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -483,11 +483,11 @@ build_info:
   output: "target/executable/annotate/singler"
   executable: "target/executable/annotate/singler/singler"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -517,7 +517,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/annotate/singler/singler b/target/executable/annotate/singler/singler
index 34ce7abe..738bcf61 100755
--- a/target/executable/annotate/singler/singler
+++ b/target/executable/annotate/singler/singler
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# singler v4.0.0
+# singler v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -467,10 +467,10 @@ RUN pip install --user --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component annotate singler"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -587,7 +587,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "singler v4.0.0"
+  echo "singler v4.0.1"
   echo ""
   echo "SingleR performs reference-based cell type annotation for single-cell RNA-seq"
   echo "data"
@@ -813,7 +813,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "singler v4.0.0"
+            echo "singler v4.0.1"
             exit
             ;;
         --input)
@@ -1185,7 +1185,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/singler:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/singler:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/annotate/svm_annotation/.config.vsh.yaml b/target/executable/annotate/svm_annotation/.config.vsh.yaml
index 5602637d..11940020 100644
--- a/target/executable/annotate/svm_annotation/.config.vsh.yaml
+++ b/target/executable/annotate/svm_annotation/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "svm_annotation"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -356,7 +356,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -403,11 +403,11 @@ build_info:
   output: "target/executable/annotate/svm_annotation"
   executable: "target/executable/annotate/svm_annotation/svm_annotation"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -437,7 +437,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/annotate/svm_annotation/svm_annotation b/target/executable/annotate/svm_annotation/svm_annotation
index 77d742aa..a3bd2ce3 100755
--- a/target/executable/annotate/svm_annotation/svm_annotation
+++ b/target/executable/annotate/svm_annotation/svm_annotation
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# svm_annotation v4.0.0
+# svm_annotation v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component annotate svm_annotation"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:38Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "svm_annotation v4.0.0"
+  echo "svm_annotation v4.0.1"
   echo ""
   echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of SVMs."
   echo ""
@@ -758,7 +758,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "svm_annotation v4.0.0"
+            echo "svm_annotation v4.0.1"
             exit
             ;;
         --input)
@@ -1069,7 +1069,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/svm_annotation:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/svm_annotation:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/cluster/leiden/.config.vsh.yaml b/target/executable/cluster/leiden/.config.vsh.yaml
index d59aff3a..7c62be98 100644
--- a/target/executable/cluster/leiden/.config.vsh.yaml
+++ b/target/executable/cluster/leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "leiden"
 namespace: "cluster"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -215,7 +215,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -258,11 +258,11 @@ build_info:
   output: "target/executable/cluster/leiden"
   executable: "target/executable/cluster/leiden/leiden"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/cluster/leiden/leiden b/target/executable/cluster/leiden/leiden
index 4ed46334..129be66d 100755
--- a/target/executable/cluster/leiden/leiden
+++ b/target/executable/cluster/leiden/leiden
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# leiden v4.0.0
+# leiden v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer"
 LABEL org.opencontainers.image.description="Companion container for running component cluster leiden"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "leiden v4.0.0"
+  echo "leiden v4.0.1"
   echo ""
   echo "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy"
   echo "framework] [Wolf18]."
@@ -685,7 +685,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "leiden v4.0.0"
+            echo "leiden v4.0.1"
             exit
             ;;
         --input)
@@ -871,7 +871,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/cluster/leiden:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/cluster/leiden:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/compression/compress_h5mu/.config.vsh.yaml b/target/executable/compression/compress_h5mu/.config.vsh.yaml
index d04b530d..ddd40b9e 100644
--- a/target/executable/compression/compress_h5mu/.config.vsh.yaml
+++ b/target/executable/compression/compress_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "compress_h5mu"
 namespace: "compression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -157,7 +157,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -198,11 +198,11 @@ build_info:
   output: "target/executable/compression/compress_h5mu"
   executable: "target/executable/compression/compress_h5mu/compress_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -232,7 +232,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/compression/compress_h5mu/compress_h5mu b/target/executable/compression/compress_h5mu/compress_h5mu
index 737b21f4..24d4fee6 100755
--- a/target/executable/compression/compress_h5mu/compress_h5mu
+++ b/target/executable/compression/compress_h5mu/compress_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# compress_h5mu v4.0.0
+# compress_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:45Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "compress_h5mu v4.0.0"
+  echo "compress_h5mu v4.0.1"
   echo ""
   echo "Compress a MuData file."
   echo ""
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "compress_h5mu v4.0.0"
+            echo "compress_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -776,7 +776,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/compress_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/compress_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/compression/tar_extract/.config.vsh.yaml b/target/executable/compression/tar_extract/.config.vsh.yaml
index f9e6e506..97bf9326 100644
--- a/target/executable/compression/tar_extract/.config.vsh.yaml
+++ b/target/executable/compression/tar_extract/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tar_extract"
 namespace: "compression"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -157,7 +157,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -170,11 +170,11 @@ build_info:
   output: "target/executable/compression/tar_extract"
   executable: "target/executable/compression/tar_extract/tar_extract"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -204,7 +204,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/compression/tar_extract/tar_extract b/target/executable/compression/tar_extract/tar_extract
index cd59763a..21767fed 100755
--- a/target/executable/compression/tar_extract/tar_extract
+++ b/target/executable/compression/tar_extract/tar_extract
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# tar_extract v4.0.0
+# tar_extract v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -446,10 +446,10 @@ function ViashDockerfile {
 FROM ubuntu:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component compression tar_extract"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:45Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -566,7 +566,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "tar_extract v4.0.0"
+  echo "tar_extract v4.0.1"
   echo ""
   echo "Extract files from a tar archive"
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "tar_extract v4.0.0"
+            echo "tar_extract v4.0.1"
             exit
             ;;
         --input)
@@ -800,7 +800,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/tar_extract:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/tar_extract:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml
index ca8ccdea..b619ed53 100644
--- a/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_10xh5_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -263,7 +263,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -305,11 +305,11 @@ build_info:
   output: "target/executable/convert/from_10xh5_to_h5mu"
   executable: "target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -339,7 +339,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu b/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu
index 9cf455b8..31a6bae6 100755
--- a/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu
+++ b/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_10xh5_to_h5mu v4.0.0
+# from_10xh5_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_10xh5_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_10xh5_to_h5mu v4.0.0"
+  echo "from_10xh5_to_h5mu v4.0.1"
   echo ""
   echo "Converts a 10x h5 into an h5mu file."
   echo ""
@@ -669,7 +669,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_10xh5_to_h5mu v4.0.0"
+            echo "from_10xh5_to_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -849,7 +849,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xh5_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xh5_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml
index f4f0612a..4b539326 100644
--- a/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_10xmtx_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -164,7 +164,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -206,11 +206,11 @@ build_info:
   output: "target/executable/convert/from_10xmtx_to_h5mu"
   executable: "target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -240,7 +240,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu b/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu
index aea8d6a4..35e46daf 100755
--- a/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu
+++ b/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_10xmtx_to_h5mu v4.0.0
+# from_10xmtx_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_10xmtx_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_10xmtx_to_h5mu v4.0.0"
+  echo "from_10xmtx_to_h5mu v4.0.1"
   echo ""
   echo "Converts a 10x mtx into an h5mu file."
   echo ""
@@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_10xmtx_to_h5mu v4.0.0"
+            echo "from_10xmtx_to_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xmtx_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xmtx_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml
index 1b6f81fd..12a8c41e 100644
--- a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml
+++ b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_bd_to_10x_molecular_barcode_tags"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -161,7 +161,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -179,11 +179,11 @@ build_info:
   output: "target/executable/convert/from_bd_to_10x_molecular_barcode_tags"
   executable: "target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -213,7 +213,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags
index 5a0be7b9..b7c00199 100755
--- a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags
+++ b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_bd_to_10x_molecular_barcode_tags v4.0.0
+# from_bd_to_10x_molecular_barcode_tags v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_bd_to_10x_molecular_barcode_tags"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_bd_to_10x_molecular_barcode_tags v4.0.0"
+  echo "from_bd_to_10x_molecular_barcode_tags v4.0.1"
   echo ""
   echo "Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format"
   echo "(UB)."
@@ -645,7 +645,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_bd_to_10x_molecular_barcode_tags v4.0.0"
+            echo "from_bd_to_10x_molecular_barcode_tags v4.0.1"
             exit
             ;;
         --input)
@@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bd_to_10x_molecular_barcode_tags:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bd_to_10x_molecular_barcode_tags:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml
index 9356b044..cc85b7e9 100644
--- a/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_bdrhap_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -190,7 +190,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -219,11 +219,11 @@ build_info:
   output: "target/executable/convert/from_bdrhap_to_h5mu"
   executable: "target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -253,7 +253,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu b/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu
index edb2d7e7..b1612a27 100755
--- a/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu
+++ b/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_bdrhap_to_h5mu v4.0.0
+# from_bdrhap_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_bdrhap_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_bdrhap_to_h5mu v4.0.0"
+  echo "from_bdrhap_to_h5mu v4.0.1"
   echo ""
   echo "Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file."
   echo ""
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_bdrhap_to_h5mu v4.0.0"
+            echo "from_bdrhap_to_h5mu v4.0.1"
             exit
             ;;
         --output_compression)
@@ -802,7 +802,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bdrhap_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bdrhap_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml
index eacb654f..786bf15f 100644
--- a/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_cellranger_multi_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -208,7 +208,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -245,11 +245,11 @@ build_info:
   output: "target/executable/convert/from_cellranger_multi_to_h5mu"
   executable: "target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -279,7 +279,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu b/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu
index ee2d098e..e5573e21 100755
--- a/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu
+++ b/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_cellranger_multi_to_h5mu v4.0.0
+# from_cellranger_multi_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_cellranger_multi_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_cellranger_multi_to_h5mu v4.0.0"
+  echo "from_cellranger_multi_to_h5mu v4.0.1"
   echo ""
   echo "Converts the output from cellranger multi to a single .h5mu file."
   echo "By default, will map the following library type names to modality names:"
@@ -671,7 +671,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_cellranger_multi_to_h5mu v4.0.0"
+            echo "from_cellranger_multi_to_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -829,7 +829,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_cellranger_multi_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_cellranger_multi_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml
index 9e5f3129..bf363fa5 100644
--- a/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5ad_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -173,7 +173,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -214,11 +214,11 @@ build_info:
   output: "target/executable/convert/from_h5ad_to_h5mu"
   executable: "target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu b/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu
index 5e1e665a..3d6183f2 100755
--- a/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu
+++ b/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_h5ad_to_h5mu v4.0.0
+# from_h5ad_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5ad_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:38Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_h5ad_to_h5mu v4.0.0"
+  echo "from_h5ad_to_h5mu v4.0.1"
   echo ""
   echo "Converts a single layer h5ad file into a single MuData object"
   echo ""
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_h5ad_to_h5mu v4.0.0"
+            echo "from_h5ad_to_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -817,7 +817,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml b/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml
index 401a0e0d..33977900 100644
--- a/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml
+++ b/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5ad_to_seurat"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -196,11 +196,11 @@ build_info:
   output: "target/executable/convert/from_h5ad_to_seurat"
   executable: "target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -230,7 +230,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat b/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat
index 1e6487dc..4b578a29 100755
--- a/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat
+++ b/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_h5ad_to_seurat v4.0.0
+# from_h5ad_to_seurat v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN
 RUN Rscript -e 'options(warn = 2); remotes::install_github(c("scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"), repos = "https://cran.rstudio.com")'
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5ad_to_seurat"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_h5ad_to_seurat v4.0.0"
+  echo "from_h5ad_to_seurat v4.0.1"
   echo ""
   echo "Converts an h5ad file into a Seurat file."
   echo ""
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_h5ad_to_seurat v4.0.0"
+            echo "from_h5ad_to_seurat v4.0.1"
             exit
             ;;
         --input)
@@ -782,7 +782,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_seurat:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_seurat:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml
index ded44a53..a1358a6d 100644
--- a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_or_h5ad_to_seurat"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -166,7 +166,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -205,11 +205,11 @@ build_info:
   output: "target/executable/convert/from_h5mu_or_h5ad_to_seurat"
   executable: "target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -239,7 +239,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat
index 415a7dc3..a7dfaf68 100755
--- a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat
+++ b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_h5mu_or_h5ad_to_seurat v4.0.0
+# from_h5mu_or_h5ad_to_seurat v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN
 RUN Rscript -e 'options(warn = 2); remotes::install_github(c("scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"), repos = "https://cran.rstudio.com")'
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_or_h5ad_to_seurat"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_h5mu_or_h5ad_to_seurat v4.0.0"
+  echo "from_h5mu_or_h5ad_to_seurat v4.0.1"
   echo ""
   echo "Converts an h5ad file or a single modality of an h5mu file into a Seurat file."
   echo ""
@@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_h5mu_or_h5ad_to_seurat v4.0.0"
+            echo "from_h5mu_or_h5ad_to_seurat v4.0.1"
             exit
             ;;
         --input)
@@ -798,7 +798,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_seurat:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_seurat:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml
index 39de1b7c..be87fab4 100644
--- a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_or_h5ad_to_tiledb"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -334,7 +334,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -381,11 +381,11 @@ build_info:
   output: "target/executable/convert/from_h5mu_or_h5ad_to_tiledb"
   executable: "target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -415,7 +415,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb
index 14c58a14..35ee8654 100755
--- a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb
+++ b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_h5mu_or_h5ad_to_tiledb v4.0.0
+# from_h5mu_or_h5ad_to_tiledb v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_or_h5ad_to_tiledb"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:38Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_h5mu_or_h5ad_to_tiledb v4.0.0"
+  echo "from_h5mu_or_h5ad_to_tiledb v4.0.1"
   echo ""
   echo "Convert a MuData or AnnData object to tiledb. Currently, transcriptome and"
   echo "protein modalities are supported."
@@ -747,7 +747,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_h5mu_or_h5ad_to_tiledb v4.0.0"
+            echo "from_h5mu_or_h5ad_to_tiledb v4.0.1"
             exit
             ;;
         --input)
@@ -1047,7 +1047,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_tiledb:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_tiledb:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml
index 4203e396..7544b982 100644
--- a/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_to_h5ad"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -174,7 +174,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -215,11 +215,11 @@ build_info:
   output: "target/executable/convert/from_h5mu_to_h5ad"
   executable: "target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -249,7 +249,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad b/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad
index ab5e7a58..e66c4e7d 100755
--- a/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad
+++ b/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_h5mu_to_h5ad v4.0.0
+# from_h5mu_to_h5ad v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_h5ad"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_h5mu_to_h5ad v4.0.0"
+  echo "from_h5mu_to_h5ad v4.0.1"
   echo ""
   echo "Converts a h5mu file into a h5ad file."
   echo ""
@@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_h5mu_to_h5ad v4.0.0"
+            echo "from_h5mu_to_h5ad v4.0.1"
             exit
             ;;
         --input)
@@ -799,7 +799,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_h5ad:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_h5ad:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml
index f2f008ee..d659bd9e 100644
--- a/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml
+++ b/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_to_seurat"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -155,7 +155,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -188,11 +188,11 @@ build_info:
   output: "target/executable/convert/from_h5mu_to_seurat"
   executable: "target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -222,7 +222,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat b/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat
index d8a19dc7..afff4690 100755
--- a/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat
+++ b/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_h5mu_to_seurat v4.0.0
+# from_h5mu_to_seurat v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN
 RUN Rscript -e 'options(warn = 2); remotes::install_github(c("pmbio/MuDataSeurat@empty-tables-and-nullable"), repos = "https://cran.rstudio.com")'
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_seurat"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:37Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_h5mu_to_seurat v4.0.0"
+  echo "from_h5mu_to_seurat v4.0.1"
   echo ""
   echo "Converts an h5mu file into a Seurat file."
   echo ""
@@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_h5mu_to_seurat v4.0.0"
+            echo "from_h5mu_to_seurat v4.0.1"
             exit
             ;;
         --input)
@@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_seurat:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_seurat:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml
index 77f9c588..605c01ce 100644
--- a/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_seurat_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -312,7 +312,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -388,11 +388,11 @@ build_info:
   output: "target/executable/convert/from_seurat_to_h5mu"
   executable: "target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -422,7 +422,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu b/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu
index 776d6f6b..2c9d0ecf 100755
--- a/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu
+++ b/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_seurat_to_h5mu v4.0.0
+# from_seurat_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -472,10 +472,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_seurat_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -592,7 +592,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_seurat_to_h5mu v4.0.0"
+  echo "from_seurat_to_h5mu v4.0.1"
   echo ""
   echo "Converts a Seurat file into an H5MU file."
   echo ""
@@ -758,7 +758,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_seurat_to_h5mu v4.0.0"
+            echo "from_seurat_to_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -1015,7 +1015,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_seurat_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_seurat_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml
index 4e6a66dc..2f9d4df8 100644
--- a/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_tiledb_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -214,7 +214,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -258,11 +258,11 @@ build_info:
   output: "target/executable/convert/from_tiledb_to_h5mu"
   executable: "target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu b/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu
index b3f212c7..ebd2551b 100755
--- a/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu
+++ b/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# from_tiledb_to_h5mu v4.0.0
+# from_tiledb_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component convert from_tiledb_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "from_tiledb_to_h5mu v4.0.0"
+  echo "from_tiledb_to_h5mu v4.0.1"
   echo ""
   echo "Input database:"
   echo "    Open a tileDB-SOMA database by URI."
@@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "from_tiledb_to_h5mu v4.0.0"
+            echo "from_tiledb_to_h5mu v4.0.1"
             exit
             ;;
         --input_uri)
@@ -866,7 +866,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_tiledb_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_tiledb_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml
index d9de3128..f54750d6 100644
--- a/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml
+++ b/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "velocyto_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -244,7 +244,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -275,11 +275,11 @@ build_info:
   output: "target/executable/convert/velocyto_to_h5mu"
   executable: "target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -309,7 +309,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu b/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu
index c5a60032..304ea347 100755
--- a/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu
+++ b/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# velocyto_to_h5mu v4.0.0
+# velocyto_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt, Angela Oliveira Pisco"
 LABEL org.opencontainers.image.description="Companion container for running component convert velocyto_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -580,7 +580,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "velocyto_to_h5mu v4.0.0"
+  echo "velocyto_to_h5mu v4.0.1"
   echo ""
   echo "Convert a velocyto loom file to a h5mu file."
   echo ""
@@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "velocyto_to_h5mu v4.0.0"
+            echo "velocyto_to_h5mu v4.0.1"
             exit
             ;;
         --input_loom)
@@ -857,7 +857,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/velocyto_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/velocyto_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/correction/cellbender_remove_background/.config.vsh.yaml b/target/executable/correction/cellbender_remove_background/.config.vsh.yaml
index d035f59a..a4ef0c81 100644
--- a/target/executable/correction/cellbender_remove_background/.config.vsh.yaml
+++ b/target/executable/correction/cellbender_remove_background/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellbender_remove_background"
 namespace: "correction"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Inputs"
   arguments:
@@ -578,7 +578,7 @@ engines:
   id: "docker"
   image: "nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -611,11 +611,11 @@ build_info:
   output: "target/executable/correction/cellbender_remove_background"
   executable: "target/executable/correction/cellbender_remove_background/cellbender_remove_background"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -645,7 +645,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/correction/cellbender_remove_background/cellbender_remove_background b/target/executable/correction/cellbender_remove_background/cellbender_remove_background
index a46d2743..36506005 100755
--- a/target/executable/correction/cellbender_remove_background/cellbender_remove_background
+++ b/target/executable/correction/cellbender_remove_background/cellbender_remove_background
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellbender_remove_background v4.0.0
+# cellbender_remove_background v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "lxml~=4.8.0" "mudata~=0.2.1" "cellbender~=0.3.0"
 
 LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:45Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellbender_remove_background v4.0.0"
+  echo "cellbender_remove_background v4.0.1"
   echo ""
   echo "Eliminating technical artifacts from high-throughput single-cell RNA sequencing"
   echo "data."
@@ -911,7 +911,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellbender_remove_background v4.0.0"
+            echo "cellbender_remove_background v4.0.1"
             exit
             ;;
         --input)
@@ -1482,7 +1482,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml
index 435e990c..ba36467a 100644
--- a/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml
+++ b/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "concatenate_h5mu"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -253,7 +253,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -300,11 +300,11 @@ build_info:
   output: "target/executable/dataflow/concatenate_h5mu"
   executable: "target/executable/dataflow/concatenate_h5mu/concatenate_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -334,7 +334,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu b/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu
index 1e15e352..83f5be2c 100755
--- a/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu
+++ b/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# concatenate_h5mu v4.0.0
+# concatenate_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component dataflow concatenate_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "concatenate_h5mu v4.0.0"
+  echo "concatenate_h5mu v4.0.1"
   echo ""
   echo "Concatenate observations from samples in several (uni- and/or multi-modal)"
   echo "MuData files into a single file."
@@ -706,7 +706,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "concatenate_h5mu v4.0.0"
+            echo "concatenate_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -935,7 +935,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/concatenate_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/concatenate_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dataflow/merge/.config.vsh.yaml b/target/executable/dataflow/merge/.config.vsh.yaml
index 34e31353..3b0ba162 100644
--- a/target/executable/dataflow/merge/.config.vsh.yaml
+++ b/target/executable/dataflow/merge/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "merge"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -163,7 +163,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -204,11 +204,11 @@ build_info:
   output: "target/executable/dataflow/merge"
   executable: "target/executable/dataflow/merge/merge"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -238,7 +238,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dataflow/merge/merge b/target/executable/dataflow/merge/merge
index 3a263e3a..952a7606 100755
--- a/target/executable/dataflow/merge/merge
+++ b/target/executable/dataflow/merge/merge
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# merge v4.0.0
+# merge v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component dataflow merge"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "merge v4.0.0"
+  echo "merge v4.0.1"
   echo ""
   echo "Combine one or more single-modality .h5mu files together into one .h5mu file."
   echo ""
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "merge v4.0.0"
+            echo "merge v4.0.1"
             exit
             ;;
         --input)
@@ -791,7 +791,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/merge:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/merge:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dataflow/split_h5mu/.config.vsh.yaml b/target/executable/dataflow/split_h5mu/.config.vsh.yaml
index 4094933a..e01ec4d2 100644
--- a/target/executable/dataflow/split_h5mu/.config.vsh.yaml
+++ b/target/executable/dataflow/split_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_h5mu"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -203,7 +203,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -244,11 +244,11 @@ build_info:
   output: "target/executable/dataflow/split_h5mu"
   executable: "target/executable/dataflow/split_h5mu/split_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -278,7 +278,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dataflow/split_h5mu/split_h5mu b/target/executable/dataflow/split_h5mu/split_h5mu
index feedb503..3f9e2a24 100755
--- a/target/executable/dataflow/split_h5mu/split_h5mu
+++ b/target/executable/dataflow/split_h5mu/split_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# split_h5mu v4.0.0
+# split_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component dataflow split_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "split_h5mu v4.0.0"
+  echo "split_h5mu v4.0.1"
   echo ""
   echo "Split the samples of a single modality from a .h5mu (multimodal) sample into"
   echo "seperate .h5mu files based on the values of an .obs column of this modality."
@@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "split_h5mu v4.0.0"
+            echo "split_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -841,7 +841,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dataflow/split_modalities/.config.vsh.yaml b/target/executable/dataflow/split_modalities/.config.vsh.yaml
index 7d93e2d7..733317f9 100644
--- a/target/executable/dataflow/split_modalities/.config.vsh.yaml
+++ b/target/executable/dataflow/split_modalities/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_modalities"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -190,7 +190,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -231,11 +231,11 @@ build_info:
   output: "target/executable/dataflow/split_modalities"
   executable: "target/executable/dataflow/split_modalities/split_modalities"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -265,7 +265,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dataflow/split_modalities/split_modalities b/target/executable/dataflow/split_modalities/split_modalities
index 7924e841..420957ee 100755
--- a/target/executable/dataflow/split_modalities/split_modalities
+++ b/target/executable/dataflow/split_modalities/split_modalities
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# split_modalities v4.0.0
+# split_modalities v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component dataflow split_modalities"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:35Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "split_modalities v4.0.0"
+  echo "split_modalities v4.0.1"
   echo ""
   echo "Split the modalities from a single .h5mu multimodal sample into seperate .h5mu"
   echo "files."
@@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "split_modalities v4.0.0"
+            echo "split_modalities v4.0.1"
             exit
             ;;
         --input)
@@ -801,7 +801,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_modalities:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_modalities:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/demux/bcl2fastq/.config.vsh.yaml b/target/executable/demux/bcl2fastq/.config.vsh.yaml
index c372864a..d0c9e831 100644
--- a/target/executable/demux/bcl2fastq/.config.vsh.yaml
+++ b/target/executable/demux/bcl2fastq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bcl2fastq"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Toni Verbeiren"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/bcl2fastq:2.20"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -196,11 +196,11 @@ build_info:
   output: "target/executable/demux/bcl2fastq"
   executable: "target/executable/demux/bcl2fastq/bcl2fastq"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -230,7 +230,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/demux/bcl2fastq/bcl2fastq b/target/executable/demux/bcl2fastq/bcl2fastq
index 453807b8..2306e871 100755
--- a/target/executable/demux/bcl2fastq/bcl2fastq
+++ b/target/executable/demux/bcl2fastq/bcl2fastq
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# bcl2fastq v4.0.0
+# bcl2fastq v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component demux bcl2fastq"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bcl2fastq v4.0.0"
+  echo "bcl2fastq v4.0.1"
   echo ""
   echo "Convert bcl files to fastq files using bcl2fastq."
   echo ""
@@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "bcl2fastq v4.0.0"
+            echo "bcl2fastq v4.0.1"
             exit
             ;;
         --input)
@@ -816,7 +816,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl2fastq:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl2fastq:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/demux/bcl_convert/.config.vsh.yaml b/target/executable/demux/bcl_convert/.config.vsh.yaml
index adf0953c..564dc106 100644
--- a/target/executable/demux/bcl_convert/.config.vsh.yaml
+++ b/target/executable/demux/bcl_convert/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bcl_convert"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Toni Verbeiren"
   roles:
@@ -250,7 +250,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/bclconvert:4.2"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -268,11 +268,11 @@ build_info:
   output: "target/executable/demux/bcl_convert"
   executable: "target/executable/demux/bcl_convert/bcl_convert"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -302,7 +302,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/demux/bcl_convert/bcl_convert b/target/executable/demux/bcl_convert/bcl_convert
index bbdfea48..b966fa21 100755
--- a/target/executable/demux/bcl_convert/bcl_convert
+++ b/target/executable/demux/bcl_convert/bcl_convert
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# bcl_convert v4.0.0
+# bcl_convert v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Toni Verbeiren, Marijke Van Moerbeke, Weiwei Schultz, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component demux bcl_convert"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:29Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bcl_convert v4.0.0"
+  echo "bcl_convert v4.0.1"
   echo ""
   echo "Convert bcl files to fastq files using bcl-convert."
   echo "Information about upgrading from bcl2fastq via"
@@ -675,7 +675,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "bcl_convert v4.0.0"
+            echo "bcl_convert v4.0.1"
             exit
             ;;
         --input)
@@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl_convert:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl_convert:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml b/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml
index ae81cf00..c205fdd8 100644
--- a/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml
+++ b/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_atac_mkfastq"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -213,7 +213,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger_atac:2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -237,11 +237,11 @@ build_info:
   output: "target/executable/demux/cellranger_atac_mkfastq"
   executable: "target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -271,7 +271,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq b/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq
index 4a9bf8c7..bc312260 100755
--- a/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq
+++ b/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_atac_mkfastq v4.0.0
+# cellranger_atac_mkfastq v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ RUN DEBIAN_FRONTEND=noninteractive apt update \
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component demux cellranger_atac_mkfastq"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_atac_mkfastq v4.0.0"
+  echo "cellranger_atac_mkfastq v4.0.1"
   echo ""
   echo "Demultiplex raw sequencing data for ATAC experiments"
   echo ""
@@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_atac_mkfastq v4.0.0"
+            echo "cellranger_atac_mkfastq v4.0.1"
             exit
             ;;
         --input)
@@ -863,7 +863,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_atac_mkfastq:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_atac_mkfastq:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml b/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml
index faa39dd3..93fff20f 100644
--- a/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml
+++ b/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_mkfastq"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -228,11 +228,11 @@ build_info:
   output: "target/executable/demux/cellranger_mkfastq"
   executable: "target/executable/demux/cellranger_mkfastq/cellranger_mkfastq"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -262,7 +262,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq b/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq
index 46b908d1..21119d46 100755
--- a/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq
+++ b/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_mkfastq v4.0.0
+# cellranger_mkfastq v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component demux cellranger_mkfastq"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:29Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_mkfastq v4.0.0"
+  echo "cellranger_mkfastq v4.0.1"
   echo ""
   echo "Demultiplex raw sequencing data"
   echo ""
@@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_mkfastq v4.0.0"
+            echo "cellranger_mkfastq v4.0.1"
             exit
             ;;
         --input)
@@ -789,7 +789,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_mkfastq:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_mkfastq:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml b/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml
index 3320f0ec..183eb61f 100644
--- a/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml
+++ b/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_pseudobulk"
 namespace: "differential_expression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -271,7 +271,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -309,11 +309,11 @@ build_info:
   output: "target/executable/differential_expression/create_pseudobulk"
   executable: "target/executable/differential_expression/create_pseudobulk/create_pseudobulk"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -343,7 +343,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/differential_expression/create_pseudobulk/create_pseudobulk b/target/executable/differential_expression/create_pseudobulk/create_pseudobulk
index a1470acb..043326a4 100755
--- a/target/executable/differential_expression/create_pseudobulk/create_pseudobulk
+++ b/target/executable/differential_expression/create_pseudobulk/create_pseudobulk
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_pseudobulk v4.0.0
+# create_pseudobulk v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Jakub Majercik, Dries De Maeyer, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component differential_expression create_pseudobulk"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pseudobulk v4.0.0"
+  echo "create_pseudobulk v4.0.1"
   echo ""
   echo "Generation of pseudobulk samples from single-cell transcriptomics data,"
   echo "by aggregating raw gene expression counts from individual cells to create"
@@ -689,7 +689,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_pseudobulk v4.0.0"
+            echo "create_pseudobulk v4.0.1"
             exit
             ;;
         --input)
@@ -902,7 +902,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/create_pseudobulk:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/create_pseudobulk:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/differential_expression/deseq2/.config.vsh.yaml b/target/executable/differential_expression/deseq2/.config.vsh.yaml
index a564083a..879a2327 100644
--- a/target/executable/differential_expression/deseq2/.config.vsh.yaml
+++ b/target/executable/differential_expression/deseq2/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "deseq2"
 namespace: "differential_expression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -294,7 +294,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -346,11 +346,11 @@ build_info:
   output: "target/executable/differential_expression/deseq2"
   executable: "target/executable/differential_expression/deseq2/deseq2"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -380,7 +380,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/differential_expression/deseq2/deseq2 b/target/executable/differential_expression/deseq2/deseq2
index 5cfe91c7..2547d01f 100755
--- a/target/executable/differential_expression/deseq2/deseq2
+++ b/target/executable/differential_expression/deseq2/deseq2
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# deseq2 v4.0.0
+# deseq2 v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -464,10 +464,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN
 RUN Rscript -e 'options(warn = 2); remotes::install_github(c("scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"), repos = "https://cran.rstudio.com")'
 LABEL org.opencontainers.image.authors="Jakub Majercik, Dorien Roosen, Dries De Maeyer, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component differential_expression deseq2"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:38Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -584,7 +584,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "deseq2 v4.0.0"
+  echo "deseq2 v4.0.1"
   echo ""
   echo "Performs differential expression analysis using DESeq2 on bulk samples or"
   echo "pseudobulk samples aggregated from single-cell data."
@@ -724,7 +724,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "deseq2 v4.0.0"
+            echo "deseq2 v4.0.1"
             exit
             ;;
         --input)
@@ -965,7 +965,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/deseq2:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/deseq2:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dimred/densmap/.config.vsh.yaml b/target/executable/dimred/densmap/.config.vsh.yaml
index 2fa921a5..8a880202 100644
--- a/target/executable/dimred/densmap/.config.vsh.yaml
+++ b/target/executable/dimred/densmap/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "densmap"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -353,7 +353,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -395,11 +395,11 @@ build_info:
   output: "target/executable/dimred/densmap"
   executable: "target/executable/dimred/densmap/densmap"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -429,7 +429,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dimred/densmap/densmap b/target/executable/dimred/densmap/densmap
index a6a16239..959a07e2 100755
--- a/target/executable/dimred/densmap/densmap
+++ b/target/executable/dimred/densmap/densmap
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# densmap v4.0.0
+# densmap v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component dimred densmap"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "densmap v4.0.0"
+  echo "densmap v4.0.1"
   echo ""
   echo "A modification of UMAP that adds an extra cost term in order to preserve"
   echo "information"
@@ -774,7 +774,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "densmap v4.0.0"
+            echo "densmap v4.0.1"
             exit
             ;;
         --input)
@@ -1069,7 +1069,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/densmap:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/densmap:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dimred/lsi/.config.vsh.yaml b/target/executable/dimred/lsi/.config.vsh.yaml
index 4fadcce1..02348afa 100644
--- a/target/executable/dimred/lsi/.config.vsh.yaml
+++ b/target/executable/dimred/lsi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "lsi"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Sarah Ouologuem"
   roles:
@@ -269,7 +269,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -314,11 +314,11 @@ build_info:
   output: "target/executable/dimred/lsi"
   executable: "target/executable/dimred/lsi/lsi"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -348,7 +348,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dimred/lsi/lsi b/target/executable/dimred/lsi/lsi
index 9b75025e..f7b4d0d0 100755
--- a/target/executable/dimred/lsi/lsi
+++ b/target/executable/dimred/lsi/lsi
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# lsi v4.0.0
+# lsi v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Sarah Ouologuem, Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component dimred lsi"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:31Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "lsi v4.0.0"
+  echo "lsi v4.0.1"
   echo ""
   echo "Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and"
   echo "singular values. Uses the implementation of scipy."
@@ -696,7 +696,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "lsi v4.0.0"
+            echo "lsi v4.0.1"
             exit
             ;;
         --input)
@@ -925,7 +925,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/lsi:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/lsi:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dimred/pca/.config.vsh.yaml b/target/executable/dimred/pca/.config.vsh.yaml
index 4337e902..00d25f73 100644
--- a/target/executable/dimred/pca/.config.vsh.yaml
+++ b/target/executable/dimred/pca/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "pca"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -240,7 +240,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -276,11 +276,11 @@ build_info:
   output: "target/executable/dimred/pca"
   executable: "target/executable/dimred/pca/pca"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -310,7 +310,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dimred/pca/pca b/target/executable/dimred/pca/pca
index b3a3f2f8..d165424b 100755
--- a/target/executable/dimred/pca/pca
+++ b/target/executable/dimred/pca/pca
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# pca v4.0.0
+# pca v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer"
 LABEL org.opencontainers.image.description="Companion container for running component dimred pca"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:31Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "pca v4.0.0"
+  echo "pca v4.0.1"
   echo ""
   echo "Computes PCA coordinates, loadings and variance decomposition. Uses the"
   echo "implementation of scikit-learn [Pedregosa11]."
@@ -689,7 +689,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "pca v4.0.0"
+            echo "pca v4.0.1"
             exit
             ;;
         --input)
@@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/pca:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/pca:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dimred/tsne/.config.vsh.yaml b/target/executable/dimred/tsne/.config.vsh.yaml
index 4208339b..9147ac2c 100644
--- a/target/executable/dimred/tsne/.config.vsh.yaml
+++ b/target/executable/dimred/tsne/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tsne"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -281,7 +281,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -323,11 +323,11 @@ build_info:
   output: "target/executable/dimred/tsne"
   executable: "target/executable/dimred/tsne/tsne"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -357,7 +357,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dimred/tsne/tsne b/target/executable/dimred/tsne/tsne
index ddb411a6..6cf4839d 100755
--- a/target/executable/dimred/tsne/tsne
+++ b/target/executable/dimred/tsne/tsne
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# tsne v4.0.0
+# tsne v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component dimred tsne"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:31Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "tsne v4.0.0"
+  echo "tsne v4.0.1"
   echo ""
   echo "t-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality"
   echo "reduction technique used to visualize high-dimensional data in a low-dimensional"
@@ -715,7 +715,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "tsne v4.0.0"
+            echo "tsne v4.0.1"
             exit
             ;;
         --input)
@@ -955,7 +955,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/tsne:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/tsne:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/dimred/umap/.config.vsh.yaml b/target/executable/dimred/umap/.config.vsh.yaml
index 9f0e31d5..444f5a08 100644
--- a/target/executable/dimred/umap/.config.vsh.yaml
+++ b/target/executable/dimred/umap/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "umap"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -294,7 +294,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -330,11 +330,11 @@ build_info:
   output: "target/executable/dimred/umap"
   executable: "target/executable/dimred/umap/umap"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -364,7 +364,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/dimred/umap/umap b/target/executable/dimred/umap/umap
index 2b48ff1c..dbf9883b 100755
--- a/target/executable/dimred/umap/umap
+++ b/target/executable/dimred/umap/umap
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# umap v4.0.0
+# umap v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer"
 LABEL org.opencontainers.image.description="Companion container for running component dimred umap"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:31Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "umap v4.0.0"
+  echo "umap v4.0.1"
   echo ""
   echo "UMAP (Uniform Manifold Approximation and Projection) is a manifold learning"
   echo "technique suitable for visualizing high-dimensional data. Besides tending to be"
@@ -726,7 +726,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "umap v4.0.0"
+            echo "umap v4.0.1"
             exit
             ;;
         --input)
@@ -977,7 +977,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/umap:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/umap:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/download/download_file/.config.vsh.yaml b/target/executable/download/download_file/.config.vsh.yaml
index 334ecf60..68f75e5d 100644
--- a/target/executable/download/download_file/.config.vsh.yaml
+++ b/target/executable/download/download_file/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "download_file"
 namespace: "download"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -146,7 +146,7 @@ engines:
   id: "docker"
   image: "bash:5.1.16"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -159,11 +159,11 @@ build_info:
   output: "target/executable/download/download_file"
   executable: "target/executable/download/download_file/download_file"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -193,7 +193,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/download/download_file/download_file b/target/executable/download/download_file/download_file
index e8146438..69ba5b3b 100755
--- a/target/executable/download/download_file/download_file
+++ b/target/executable/download/download_file/download_file
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# download_file v4.0.0
+# download_file v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ FROM bash:5.1.16
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component download download_file"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:36Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "download_file v4.0.0"
+  echo "download_file v4.0.1"
   echo ""
   echo "Download a file."
   echo ""
@@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "download_file v4.0.0"
+            echo "download_file v4.0.1"
             exit
             ;;
         --input)
@@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/download_file:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/download_file:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml b/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml
index c344d047..9f3d977d 100644
--- a/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml
+++ b/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "align_query_reference"
 namespace: "feature_annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -476,7 +476,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -517,11 +517,11 @@ build_info:
   output: "target/executable/feature_annotation/align_query_reference"
   executable: "target/executable/feature_annotation/align_query_reference/align_query_reference"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -551,7 +551,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/feature_annotation/align_query_reference/align_query_reference b/target/executable/feature_annotation/align_query_reference/align_query_reference
index e38eca47..47be917f 100755
--- a/target/executable/feature_annotation/align_query_reference/align_query_reference
+++ b/target/executable/feature_annotation/align_query_reference/align_query_reference
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# align_query_reference v4.0.0
+# align_query_reference v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component feature_annotation align_query_reference"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "align_query_reference v4.0.0"
+  echo "align_query_reference v4.0.1"
   echo ""
   echo "Alignment of a query and reference dataset by:"
   echo "* Alignment of layers"
@@ -835,7 +835,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "align_query_reference v4.0.0"
+            echo "align_query_reference v4.0.1"
             exit
             ;;
         --input)
@@ -1260,7 +1260,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/align_query_reference:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/align_query_reference:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml b/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml
index 8d20c042..f3f1a771 100644
--- a/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml
+++ b/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "highly_variable_features_scanpy"
 namespace: "feature_annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -342,7 +342,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -381,11 +381,11 @@ build_info:
   output: "target/executable/feature_annotation/highly_variable_features_scanpy"
   executable: "target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -415,7 +415,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy b/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy
index 83cfa313..b056d069 100755
--- a/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy
+++ b/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# highly_variable_features_scanpy v4.0.0
+# highly_variable_features_scanpy v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component feature_annotation highly_variable_features_scanpy"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:29Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "highly_variable_features_scanpy v4.0.0"
+  echo "highly_variable_features_scanpy v4.0.1"
   echo ""
   echo "Annotate highly variable features [Satija15] [Zheng17] [Stuart19]."
   echo ""
@@ -753,7 +753,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "highly_variable_features_scanpy v4.0.0"
+            echo "highly_variable_features_scanpy v4.0.1"
             exit
             ;;
         --input)
@@ -1031,7 +1031,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/highly_variable_features_scanpy:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/highly_variable_features_scanpy:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml
index 36381ca4..0959d0e5 100644
--- a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml
+++ b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "score_genes_cell_cycle_scanpy"
 namespace: "feature_annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -367,7 +367,7 @@ engines:
   id: "docker"
   image: "python:3.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -399,11 +399,11 @@ build_info:
   output: "target/executable/feature_annotation/score_genes_cell_cycle_scanpy"
   executable: "target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -433,7 +433,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy
index 62df574e..dc158e3e 100755
--- a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy
+++ b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# score_genes_cell_cycle_scanpy v4.0.0
+# score_genes_cell_cycle_scanpy v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -456,10 +456,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component feature_annotation score_genes_cell_cycle_scanpy"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:29Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "score_genes_cell_cycle_scanpy v4.0.0"
+  echo "score_genes_cell_cycle_scanpy v4.0.1"
   echo ""
   echo "Calculates the score associated to S phase and G2M phase and annotates the cell"
   echo "cycle phase for each cell, as implemented by scanpy."
@@ -748,7 +748,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "score_genes_cell_cycle_scanpy v4.0.0"
+            echo "score_genes_cell_cycle_scanpy v4.0.1"
             exit
             ;;
         --input)
@@ -1055,7 +1055,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_cell_cycle_scanpy:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_cell_cycle_scanpy:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml b/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml
index 0497e00c..49181863 100644
--- a/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml
+++ b/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "score_genes_scanpy"
 namespace: "feature_annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -256,7 +256,7 @@ engines:
   id: "docker"
   image: "python:3.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -288,11 +288,11 @@ build_info:
   output: "target/executable/feature_annotation/score_genes_scanpy"
   executable: "target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -322,7 +322,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy b/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy
index 02dac6b2..ee844f33 100755
--- a/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy
+++ b/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# score_genes_scanpy v4.0.0
+# score_genes_scanpy v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -456,10 +456,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component feature_annotation score_genes_scanpy"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:29Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "score_genes_scanpy v4.0.0"
+  echo "score_genes_scanpy v4.0.1"
   echo ""
   echo "Calculates the score of a set of genes for each cell, as implemented by scanpy."
   echo "The score is the average expression of a set of genes subtracted with the"
@@ -719,7 +719,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "score_genes_scanpy v4.0.0"
+            echo "score_genes_scanpy v4.0.1"
             exit
             ;;
         --input)
@@ -987,7 +987,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_scanpy:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_scanpy:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/files/make_params/.config.vsh.yaml b/target/executable/files/make_params/.config.vsh.yaml
index f70744f4..557a637e 100644
--- a/target/executable/files/make_params/.config.vsh.yaml
+++ b/target/executable/files/make_params/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "make_params"
 namespace: "files"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -223,7 +223,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/randpy:r4.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -236,11 +236,11 @@ build_info:
   output: "target/executable/files/make_params"
   executable: "target/executable/files/make_params/make_params"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -270,7 +270,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/files/make_params/make_params b/target/executable/files/make_params/make_params
index 97dd366a..6c254f7d 100755
--- a/target/executable/files/make_params/make_params
+++ b/target/executable/files/make_params/make_params
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# make_params v4.0.0
+# make_params v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -451,10 +451,10 @@ FROM ghcr.io/data-intuitive/randpy:r4.0
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component files make_params"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -571,7 +571,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "make_params v4.0.0"
+  echo "make_params v4.0.1"
   echo ""
   echo "Looks for files in a directory and turn it in a params file."
   echo ""
@@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "make_params v4.0.0"
+            echo "make_params v4.0.1"
             exit
             ;;
         --base_dir)
@@ -843,7 +843,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/files/make_params:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/files/make_params:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/delimit_fraction/.config.vsh.yaml b/target/executable/filter/delimit_fraction/.config.vsh.yaml
index b5a50ca4..fd99c482 100644
--- a/target/executable/filter/delimit_fraction/.config.vsh.yaml
+++ b/target/executable/filter/delimit_fraction/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "delimit_fraction"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -219,7 +219,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -260,11 +260,11 @@ build_info:
   output: "target/executable/filter/delimit_fraction"
   executable: "target/executable/filter/delimit_fraction/delimit_fraction"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -294,7 +294,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/delimit_fraction/delimit_fraction b/target/executable/filter/delimit_fraction/delimit_fraction
index c45d5c39..f3f2ce13 100755
--- a/target/executable/filter/delimit_fraction/delimit_fraction
+++ b/target/executable/filter/delimit_fraction/delimit_fraction
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# delimit_fraction v4.0.0
+# delimit_fraction v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component filter delimit_fraction"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:42Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "delimit_fraction v4.0.0"
+  echo "delimit_fraction v4.0.1"
   echo ""
   echo "Turns a column containing values between 0 and 1 into a boolean column based on"
   echo "thresholds."
@@ -680,7 +680,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "delimit_fraction v4.0.0"
+            echo "delimit_fraction v4.0.1"
             exit
             ;;
         --input)
@@ -859,7 +859,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_fraction:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_fraction:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/do_filter/.config.vsh.yaml b/target/executable/filter/do_filter/.config.vsh.yaml
index 40c13d76..3735fca7 100644
--- a/target/executable/filter/do_filter/.config.vsh.yaml
+++ b/target/executable/filter/do_filter/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "do_filter"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -193,7 +193,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -228,11 +228,11 @@ build_info:
   output: "target/executable/filter/do_filter"
   executable: "target/executable/filter/do_filter/do_filter"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -262,7 +262,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/do_filter/do_filter b/target/executable/filter/do_filter/do_filter
index 59bdf824..4b618db6 100755
--- a/target/executable/filter/do_filter/do_filter
+++ b/target/executable/filter/do_filter/do_filter
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# do_filter v4.0.0
+# do_filter v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component filter do_filter"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:41Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "do_filter v4.0.0"
+  echo "do_filter v4.0.1"
   echo ""
   echo "Remove observations and variables based on specified .obs and .var columns."
   echo ""
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "do_filter v4.0.0"
+            echo "do_filter v4.0.1"
             exit
             ;;
         --input)
@@ -831,7 +831,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/do_filter:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/do_filter:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/filter_with_counts/.config.vsh.yaml b/target/executable/filter/filter_with_counts/.config.vsh.yaml
index 258aa111..49262043 100644
--- a/target/executable/filter/filter_with_counts/.config.vsh.yaml
+++ b/target/executable/filter/filter_with_counts/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_with_counts"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -280,7 +280,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -321,11 +321,11 @@ build_info:
   output: "target/executable/filter/filter_with_counts"
   executable: "target/executable/filter/filter_with_counts/filter_with_counts"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -355,7 +355,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/filter_with_counts/filter_with_counts b/target/executable/filter/filter_with_counts/filter_with_counts
index a461fa60..94206ae3 100755
--- a/target/executable/filter/filter_with_counts/filter_with_counts
+++ b/target/executable/filter/filter_with_counts/filter_with_counts
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# filter_with_counts v4.0.0
+# filter_with_counts v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_counts"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:43Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "filter_with_counts v4.0.0"
+  echo "filter_with_counts v4.0.1"
   echo ""
   echo "Filter scRNA-seq data based on the primary QC metrics."
   echo "This is based on both the UMI counts, the gene counts"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "filter_with_counts v4.0.0"
+            echo "filter_with_counts v4.0.1"
             exit
             ;;
         --input)
@@ -933,7 +933,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_counts:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_counts:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/filter_with_pattern/.config.vsh.yaml b/target/executable/filter/filter_with_pattern/.config.vsh.yaml
index 316b16e4..54b18dcf 100644
--- a/target/executable/filter/filter_with_pattern/.config.vsh.yaml
+++ b/target/executable/filter/filter_with_pattern/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_with_pattern"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -211,7 +211,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -246,11 +246,11 @@ build_info:
   output: "target/executable/filter/filter_with_pattern"
   executable: "target/executable/filter/filter_with_pattern/filter_with_pattern"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/filter_with_pattern/filter_with_pattern b/target/executable/filter/filter_with_pattern/filter_with_pattern
index bb760b8d..12332387 100755
--- a/target/executable/filter/filter_with_pattern/filter_with_pattern
+++ b/target/executable/filter/filter_with_pattern/filter_with_pattern
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# filter_with_pattern v4.0.0
+# filter_with_pattern v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_pattern"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:42Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "filter_with_pattern v4.0.0"
+  echo "filter_with_pattern v4.0.1"
   echo ""
   echo "Filter a MuData object based on gene names using a regex."
   echo ""
@@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "filter_with_pattern v4.0.0"
+            echo "filter_with_pattern v4.0.1"
             exit
             ;;
         --input)
@@ -853,7 +853,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_pattern:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_pattern:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/filter_with_scrublet/.config.vsh.yaml b/target/executable/filter/filter_with_scrublet/.config.vsh.yaml
index a3f3e671..915e7234 100644
--- a/target/executable/filter/filter_with_scrublet/.config.vsh.yaml
+++ b/target/executable/filter/filter_with_scrublet/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_with_scrublet"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -333,7 +333,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -378,11 +378,11 @@ build_info:
   output: "target/executable/filter/filter_with_scrublet"
   executable: "target/executable/filter/filter_with_scrublet/filter_with_scrublet"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -412,7 +412,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/filter_with_scrublet/filter_with_scrublet b/target/executable/filter/filter_with_scrublet/filter_with_scrublet
index 153bc081..6eaf3a99 100755
--- a/target/executable/filter/filter_with_scrublet/filter_with_scrublet
+++ b/target/executable/filter/filter_with_scrublet/filter_with_scrublet
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# filter_with_scrublet v4.0.0
+# filter_with_scrublet v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_scrublet"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:42Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env NUMBA_CACHE_DIR=/tmp)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "filter_with_scrublet v4.0.0"
+  echo "filter_with_scrublet v4.0.1"
   echo ""
   echo "Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019)."
   echo "The method tests for potential doublets by using the expression profiles of"
@@ -752,7 +752,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "filter_with_scrublet v4.0.0"
+            echo "filter_with_scrublet v4.0.1"
             exit
             ;;
         --input)
@@ -1029,7 +1029,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_scrublet:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_scrublet:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/intersect_obs/.config.vsh.yaml b/target/executable/filter/intersect_obs/.config.vsh.yaml
index 135adfe7..f90fab3c 100644
--- a/target/executable/filter/intersect_obs/.config.vsh.yaml
+++ b/target/executable/filter/intersect_obs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "intersect_obs"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -183,7 +183,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -218,11 +218,11 @@ build_info:
   output: "target/executable/filter/intersect_obs"
   executable: "target/executable/filter/intersect_obs/intersect_obs"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -252,7 +252,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/intersect_obs/intersect_obs b/target/executable/filter/intersect_obs/intersect_obs
index 0d02684d..8dfbd465 100755
--- a/target/executable/filter/intersect_obs/intersect_obs
+++ b/target/executable/filter/intersect_obs/intersect_obs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# intersect_obs v4.0.0
+# intersect_obs v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Isabelle Bergiers"
 LABEL org.opencontainers.image.description="Companion container for running component filter intersect_obs"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:42Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "intersect_obs v4.0.0"
+  echo "intersect_obs v4.0.1"
   echo ""
   echo "Create an intersection between two or more modalities."
   echo ""
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "intersect_obs v4.0.0"
+            echo "intersect_obs v4.0.1"
             exit
             ;;
         --input)
@@ -796,7 +796,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/intersect_obs:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/intersect_obs:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/remove_modality/.config.vsh.yaml b/target/executable/filter/remove_modality/.config.vsh.yaml
index d40e2fb8..47b7dcf1 100644
--- a/target/executable/filter/remove_modality/.config.vsh.yaml
+++ b/target/executable/filter/remove_modality/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "remove_modality"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -163,7 +163,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -198,11 +198,11 @@ build_info:
   output: "target/executable/filter/remove_modality"
   executable: "target/executable/filter/remove_modality/remove_modality"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -232,7 +232,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/remove_modality/remove_modality b/target/executable/filter/remove_modality/remove_modality
index d60dfb0c..0fdb9aa0 100755
--- a/target/executable/filter/remove_modality/remove_modality
+++ b/target/executable/filter/remove_modality/remove_modality
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# remove_modality v4.0.0
+# remove_modality v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component filter remove_modality"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:41Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "remove_modality v4.0.0"
+  echo "remove_modality v4.0.1"
   echo ""
   echo "Remove a modality from a .h5mu file"
   echo ""
@@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "remove_modality v4.0.0"
+            echo "remove_modality v4.0.1"
             exit
             ;;
         --input)
@@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/remove_modality:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/remove_modality:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/subset_h5mu/.config.vsh.yaml b/target/executable/filter/subset_h5mu/.config.vsh.yaml
index 8b42921e..98135640 100644
--- a/target/executable/filter/subset_h5mu/.config.vsh.yaml
+++ b/target/executable/filter/subset_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "subset_h5mu"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -177,7 +177,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -212,11 +212,11 @@ build_info:
   output: "target/executable/filter/subset_h5mu"
   executable: "target/executable/filter/subset_h5mu/subset_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -246,7 +246,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/subset_h5mu/subset_h5mu b/target/executable/filter/subset_h5mu/subset_h5mu
index bebfc551..28c6ca3c 100755
--- a/target/executable/filter/subset_h5mu/subset_h5mu
+++ b/target/executable/filter/subset_h5mu/subset_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# subset_h5mu v4.0.0
+# subset_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component filter subset_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:41Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "subset_h5mu v4.0.0"
+  echo "subset_h5mu v4.0.1"
   echo ""
   echo "Create a subset of a mudata file by selecting the first number of observations"
   echo ""
@@ -657,7 +657,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "subset_h5mu v4.0.0"
+            echo "subset_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -803,7 +803,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/filter/subset_obsp/.config.vsh.yaml b/target/executable/filter/subset_obsp/.config.vsh.yaml
index 542091e4..a6f9cccc 100644
--- a/target/executable/filter/subset_obsp/.config.vsh.yaml
+++ b/target/executable/filter/subset_obsp/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "subset_obsp"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -207,7 +207,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -248,11 +248,11 @@ build_info:
   output: "target/executable/filter/subset_obsp"
   executable: "target/executable/filter/subset_obsp/subset_obsp"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -282,7 +282,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/filter/subset_obsp/subset_obsp b/target/executable/filter/subset_obsp/subset_obsp
index 742edfa7..6f6e14ed 100755
--- a/target/executable/filter/subset_obsp/subset_obsp
+++ b/target/executable/filter/subset_obsp/subset_obsp
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# subset_obsp v4.0.0
+# subset_obsp v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component filter subset_obsp"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:43Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "subset_obsp v4.0.0"
+  echo "subset_obsp v4.0.1"
   echo ""
   echo "Create a subset of an .obsp field in a mudata file, by filtering the columns"
   echo "based on the values of an .obs column. The resulting subset is moved to an .obsm"
@@ -672,7 +672,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "subset_obsp v4.0.0"
+            echo "subset_obsp v4.0.1"
             exit
             ;;
         --output_compression)
@@ -851,7 +851,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_obsp:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_obsp:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/bcftools/.config.vsh.yaml b/target/executable/genetic_demux/bcftools/.config.vsh.yaml
index 0d67bbd4..79544fcb 100644
--- a/target/executable/genetic_demux/bcftools/.config.vsh.yaml
+++ b/target/executable/genetic_demux/bcftools/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bcftools"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -195,11 +195,11 @@ build_info:
   output: "target/executable/genetic_demux/bcftools"
   executable: "target/executable/genetic_demux/bcftools/bcftools"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -229,7 +229,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/bcftools/bcftools b/target/executable/genetic_demux/bcftools/bcftools
index 87ffb55f..e73dcf1f 100755
--- a/target/executable/genetic_demux/bcftools/bcftools
+++ b/target/executable/genetic_demux/bcftools/bcftools
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# bcftools v4.0.0
+# bcftools v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ RUN apt-get update && \
 RUN wget https://github.com/samtools/bcftools/releases/download/1.16/bcftools-1.16.tar.bz2 -O bcftools.tar.bz2 && tar -xjvf bcftools.tar.bz2 && cd bcftools-1.16 && make prefix=/usr/local install
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux bcftools"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:28Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bcftools v4.0.0"
+  echo "bcftools v4.0.1"
   echo ""
   echo "Filter the variants called by freebayes or cellSNP"
   echo ""
@@ -650,7 +650,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "bcftools v4.0.0"
+            echo "bcftools v4.0.1"
             exit
             ;;
         --vcf)
@@ -790,7 +790,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/bcftools:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/bcftools:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/cellsnp/.config.vsh.yaml b/target/executable/genetic_demux/cellsnp/.config.vsh.yaml
index 42c3f520..55a0aa10 100644
--- a/target/executable/genetic_demux/cellsnp/.config.vsh.yaml
+++ b/target/executable/genetic_demux/cellsnp/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellsnp"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -327,7 +327,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -369,11 +369,11 @@ build_info:
   output: "target/executable/genetic_demux/cellsnp"
   executable: "target/executable/genetic_demux/cellsnp/cellsnp"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -403,7 +403,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/cellsnp/cellsnp b/target/executable/genetic_demux/cellsnp/cellsnp
index 37cbbe30..2e57f1ed 100755
--- a/target/executable/genetic_demux/cellsnp/cellsnp
+++ b/target/executable/genetic_demux/cellsnp/cellsnp
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellsnp v4.0.0
+# cellsnp v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -456,10 +456,10 @@ RUN wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.t
 RUN git clone https://github.com/single-cell-genetics/cellsnp-lite.git && cd cellsnp-lite && autoreconf -iv && ./configure --with-htslib=/htslib-1.16 && make && make install
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux cellsnp"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:27Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellsnp v4.0.0"
+  echo "cellsnp v4.0.1"
   echo ""
   echo "cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq"
   echo "data. It can be directly used for donor deconvolution in multiplexed single-cell"
@@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellsnp v4.0.0"
+            echo "cellsnp v4.0.1"
             exit
             ;;
         --sam_file)
@@ -1056,7 +1056,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/cellsnp:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/cellsnp:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/demuxlet/.config.vsh.yaml b/target/executable/genetic_demux/demuxlet/.config.vsh.yaml
index 192f9590..d57a893d 100644
--- a/target/executable/genetic_demux/demuxlet/.config.vsh.yaml
+++ b/target/executable/genetic_demux/demuxlet/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "demuxlet"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -406,7 +406,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -455,11 +455,11 @@ build_info:
   output: "target/executable/genetic_demux/demuxlet"
   executable: "target/executable/genetic_demux/demuxlet/demuxlet"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -489,7 +489,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/demuxlet/demuxlet b/target/executable/genetic_demux/demuxlet/demuxlet
index 3bf2bb77..a7f93cd7 100755
--- a/target/executable/genetic_demux/demuxlet/demuxlet
+++ b/target/executable/genetic_demux/demuxlet/demuxlet
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# demuxlet v4.0.0
+# demuxlet v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -460,10 +460,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux demuxlet"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:26Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -580,7 +580,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "demuxlet v4.0.0"
+  echo "demuxlet v4.0.1"
   echo ""
   echo "Demuxlet is a software tool to deconvolute sample identity and identify"
   echo "multiplets when"
@@ -782,7 +782,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "demuxlet v4.0.0"
+            echo "demuxlet v4.0.1"
             exit
             ;;
         --sam)
@@ -1187,7 +1187,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/demuxlet:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/demuxlet:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml b/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml
index 8d56f953..a135f2ba 100644
--- a/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml
+++ b/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "dsc_pileup"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -329,7 +329,7 @@ engines:
   id: "docker"
   image: "ubuntu:20.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -367,11 +367,11 @@ build_info:
   output: "target/executable/genetic_demux/dsc_pileup"
   executable: "target/executable/genetic_demux/dsc_pileup/dsc_pileup"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -401,7 +401,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/dsc_pileup/dsc_pileup b/target/executable/genetic_demux/dsc_pileup/dsc_pileup
index aa1b7cd4..3993eb6b 100755
--- a/target/executable/genetic_demux/dsc_pileup/dsc_pileup
+++ b/target/executable/genetic_demux/dsc_pileup/dsc_pileup
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# dsc_pileup v4.0.0
+# dsc_pileup v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -456,10 +456,10 @@ RUN git clone https://github.com/samtools/htslib.git /tmp/htslib && cd /tmp/htsl
 RUN git clone --depth 1 https://github.com/statgen/popscle.git /tmp/popscle && mkdir -p /tmp/popscle/build && cd /tmp/popscle/build && cmake .. && make && cp /tmp/popscle/bin/popscle /usr/local/bin
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux dsc_pileup"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:27Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "dsc_pileup v4.0.0"
+  echo "dsc_pileup v4.0.1"
   echo ""
   echo "Dsc-pileup is a software tool to pileup reads and corresponding base quality"
   echo "for each overlapping SNPs and each barcode. By using pileup files,"
@@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "dsc_pileup v4.0.0"
+            echo "dsc_pileup v4.0.1"
             exit
             ;;
         --sam)
@@ -1058,7 +1058,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/dsc_pileup:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/dsc_pileup:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/freebayes/.config.vsh.yaml b/target/executable/genetic_demux/freebayes/.config.vsh.yaml
index 55164b81..67da6502 100644
--- a/target/executable/genetic_demux/freebayes/.config.vsh.yaml
+++ b/target/executable/genetic_demux/freebayes/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "freebayes"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -774,7 +774,7 @@ engines:
   id: "docker"
   image: "debian:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -792,11 +792,11 @@ build_info:
   output: "target/executable/genetic_demux/freebayes"
   executable: "target/executable/genetic_demux/freebayes/freebayes"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -826,7 +826,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/freebayes/freebayes b/target/executable/genetic_demux/freebayes/freebayes
index 00fae42d..925d94fc 100755
--- a/target/executable/genetic_demux/freebayes/freebayes
+++ b/target/executable/genetic_demux/freebayes/freebayes
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# freebayes v4.0.0
+# freebayes v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux freebayes"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:27Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "freebayes v4.0.0"
+  echo "freebayes v4.0.1"
   echo ""
   echo "Freebayes is a Bayesian genetic variant detector designed to"
   echo "find small polymorphisms, specifically SNPs."
@@ -1021,7 +1021,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "freebayes v4.0.0"
+            echo "freebayes v4.0.1"
             exit
             ;;
         --bam)
@@ -1769,7 +1769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freebayes:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freebayes:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml b/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml
index b89ffec8..fa3dcd2a 100644
--- a/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml
+++ b/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "freemuxlet"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -322,7 +322,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -371,11 +371,11 @@ build_info:
   output: "target/executable/genetic_demux/freemuxlet"
   executable: "target/executable/genetic_demux/freemuxlet/freemuxlet"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -405,7 +405,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/freemuxlet/freemuxlet b/target/executable/genetic_demux/freemuxlet/freemuxlet
index 4b6d4f06..c478957c 100755
--- a/target/executable/genetic_demux/freemuxlet/freemuxlet
+++ b/target/executable/genetic_demux/freemuxlet/freemuxlet
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# freemuxlet v4.0.0
+# freemuxlet v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -460,10 +460,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux freemuxlet"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:28Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -580,7 +580,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "freemuxlet v4.0.0"
+  echo "freemuxlet v4.0.1"
   echo ""
   echo "Freemuxlet is a software tool to deconvolute sample identity and identify"
   echo "multiplets when"
@@ -742,7 +742,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "freemuxlet v4.0.0"
+            echo "freemuxlet v4.0.1"
             exit
             ;;
         --plp)
@@ -1052,7 +1052,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freemuxlet:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freemuxlet:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/samtools/.config.vsh.yaml b/target/executable/genetic_demux/samtools/.config.vsh.yaml
index 1763dfb3..9eb1979f 100644
--- a/target/executable/genetic_demux/samtools/.config.vsh.yaml
+++ b/target/executable/genetic_demux/samtools/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -138,7 +138,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -173,11 +173,11 @@ build_info:
   output: "target/executable/genetic_demux/samtools"
   executable: "target/executable/genetic_demux/samtools/samtools"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -207,7 +207,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/samtools/samtools b/target/executable/genetic_demux/samtools/samtools
index 0527ef29..9c641238 100755
--- a/target/executable/genetic_demux/samtools/samtools
+++ b/target/executable/genetic_demux/samtools/samtools
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# samtools v4.0.0
+# samtools v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux samtools"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:26Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "samtools v4.0.0"
+  echo "samtools v4.0.1"
   echo ""
   echo "Filter the BAM according to the instruction of scSplit via Samtools."
   echo ""
@@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "samtools v4.0.0"
+            echo "samtools v4.0.1"
             exit
             ;;
         --bam)
@@ -752,7 +752,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/samtools:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/samtools:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/scsplit/.config.vsh.yaml b/target/executable/genetic_demux/scsplit/.config.vsh.yaml
index 11b0b922..bd75ed0a 100644
--- a/target/executable/genetic_demux/scsplit/.config.vsh.yaml
+++ b/target/executable/genetic_demux/scsplit/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scsplit"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -265,7 +265,7 @@ engines:
   id: "docker"
   image: "python:3.13"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -301,11 +301,11 @@ build_info:
   output: "target/executable/genetic_demux/scsplit"
   executable: "target/executable/genetic_demux/scsplit/scsplit"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -335,7 +335,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/scsplit/scsplit b/target/executable/genetic_demux/scsplit/scsplit
index 604fb569..d54144f2 100755
--- a/target/executable/genetic_demux/scsplit/scsplit
+++ b/target/executable/genetic_demux/scsplit/scsplit
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scsplit v4.0.0
+# scsplit v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 RUN git clone https://github.com/jon-xu/scSplit && cd scSplit && git apply /opt/scSplit.patch && cp scSplit /usr/local/bin && cd .. && rm -rf scSplit
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux scsplit"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:28Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:07Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scsplit v4.0.0"
+  echo "scsplit v4.0.1"
   echo ""
   echo "scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq,"
   echo "using a hidden state model for identifying genetically distinct samples within a"
@@ -702,7 +702,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scsplit v4.0.0"
+            echo "scsplit v4.0.1"
             exit
             ;;
         --vcf)
@@ -958,7 +958,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/scsplit:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/scsplit:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/souporcell/.config.vsh.yaml b/target/executable/genetic_demux/souporcell/.config.vsh.yaml
index d02c72fe..e2e44fbc 100644
--- a/target/executable/genetic_demux/souporcell/.config.vsh.yaml
+++ b/target/executable/genetic_demux/souporcell/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "souporcell"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -272,7 +272,7 @@ engines:
   id: "docker"
   image: "cumulusprod/souporcell:2022.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -285,11 +285,11 @@ build_info:
   output: "target/executable/genetic_demux/souporcell"
   executable: "target/executable/genetic_demux/souporcell/souporcell"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -319,7 +319,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/souporcell/souporcell b/target/executable/genetic_demux/souporcell/souporcell
index 02540559..d3aa0952 100755
--- a/target/executable/genetic_demux/souporcell/souporcell
+++ b/target/executable/genetic_demux/souporcell/souporcell
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# souporcell v4.0.0
+# souporcell v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ FROM cumulusprod/souporcell:2022.12
 ENTRYPOINT []
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux souporcell"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:27Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "souporcell v4.0.0"
+  echo "souporcell v4.0.1"
   echo ""
   echo "souporcell is a method for clustering mixed-genotype scRNAseq experiments by"
   echo "individual."
@@ -698,7 +698,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "souporcell v4.0.0"
+            echo "souporcell v4.0.1"
             exit
             ;;
         --fasta)
@@ -959,7 +959,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/souporcell:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/souporcell:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/genetic_demux/vireo/.config.vsh.yaml b/target/executable/genetic_demux/vireo/.config.vsh.yaml
index 04e5136b..1707f6b8 100644
--- a/target/executable/genetic_demux/vireo/.config.vsh.yaml
+++ b/target/executable/genetic_demux/vireo/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "vireo"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -285,7 +285,7 @@ engines:
   id: "docker"
   image: "python:3.13"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -305,11 +305,11 @@ build_info:
   output: "target/executable/genetic_demux/vireo"
   executable: "target/executable/genetic_demux/vireo/vireo"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -339,7 +339,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/genetic_demux/vireo/vireo b/target/executable/genetic_demux/vireo/vireo
index 8cec3632..e779495d 100755
--- a/target/executable/genetic_demux/vireo/vireo
+++ b/target/executable/genetic_demux/vireo/vireo
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# vireo v4.0.0
+# vireo v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Xichen Wu"
 LABEL org.opencontainers.image.description="Companion container for running component genetic_demux vireo"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:28Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "vireo v4.0.0"
+  echo "vireo v4.0.1"
   echo ""
   echo "Vireo is primarily designed for demultiplexing cells into donors by modelling of"
   echo "expressed alleles."
@@ -706,7 +706,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "vireo v4.0.0"
+            echo "vireo v4.0.1"
             exit
             ;;
         --cell_data)
@@ -979,7 +979,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/vireo:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/vireo:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/integrate/harmonypy/.config.vsh.yaml b/target/executable/integrate/harmonypy/.config.vsh.yaml
index 9c49cfb5..77e4b4b8 100644
--- a/target/executable/integrate/harmonypy/.config.vsh.yaml
+++ b/target/executable/integrate/harmonypy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "harmonypy"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -232,7 +232,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -275,11 +275,11 @@ build_info:
   output: "target/executable/integrate/harmonypy"
   executable: "target/executable/integrate/harmonypy/harmonypy"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -309,7 +309,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/integrate/harmonypy/harmonypy b/target/executable/integrate/harmonypy/harmonypy
index 2f84f430..94fc318b 100755
--- a/target/executable/integrate/harmonypy/harmonypy
+++ b/target/executable/integrate/harmonypy/harmonypy
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# harmonypy v4.0.0
+# harmonypy v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component integrate harmonypy"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:24Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:29Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "harmonypy v4.0.0"
+  echo "harmonypy v4.0.1"
   echo ""
   echo "Performs Harmony integration based as described in"
   echo "https://github.com/immunogenomics/harmony. Based on an implementation in python"
@@ -676,7 +676,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "harmonypy v4.0.0"
+            echo "harmonypy v4.0.1"
             exit
             ;;
         --input)
@@ -879,7 +879,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/harmonypy:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/harmonypy:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/integrate/scanorama/.config.vsh.yaml b/target/executable/integrate/scanorama/.config.vsh.yaml
index 856c9afb..61286ec0 100644
--- a/target/executable/integrate/scanorama/.config.vsh.yaml
+++ b/target/executable/integrate/scanorama/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanorama"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -269,7 +269,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -313,11 +313,11 @@ build_info:
   output: "target/executable/integrate/scanorama"
   executable: "target/executable/integrate/scanorama/scanorama"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -347,7 +347,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/integrate/scanorama/scanorama b/target/executable/integrate/scanorama/scanorama
index e919891c..0328014b 100755
--- a/target/executable/integrate/scanorama/scanorama
+++ b/target/executable/integrate/scanorama/scanorama
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scanorama v4.0.0
+# scanorama v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integrate scanorama"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:25Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scanorama v4.0.0"
+  echo "scanorama v4.0.1"
   echo ""
   echo "Use Scanorama to integrate different experiments."
   echo ""
@@ -696,7 +696,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scanorama v4.0.0"
+            echo "scanorama v4.0.1"
             exit
             ;;
         --input)
@@ -931,7 +931,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scanorama:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scanorama:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/integrate/scarches/.config.vsh.yaml b/target/executable/integrate/scarches/.config.vsh.yaml
index 442a9f22..f3c9a512 100644
--- a/target/executable/integrate/scarches/.config.vsh.yaml
+++ b/target/executable/integrate/scarches/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scarches"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -442,7 +442,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -474,11 +474,11 @@ build_info:
   output: "target/executable/integrate/scarches"
   executable: "target/executable/integrate/scarches/scarches"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -508,7 +508,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/integrate/scarches/scarches b/target/executable/integrate/scarches/scarches
index c4d7c7f2..1e5dd1da 100755
--- a/target/executable/integrate/scarches/scarches
+++ b/target/executable/integrate/scarches/scarches
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scarches v4.0.0
+# scarches v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component integrate scarches"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:25Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scarches v4.0.0"
+  echo "scarches v4.0.1"
   echo ""
   echo "Performs reference mapping with scArches"
   echo ""
@@ -789,7 +789,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scarches v4.0.0"
+            echo "scarches v4.0.1"
             exit
             ;;
         --input)
@@ -1196,7 +1196,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scarches:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scarches:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/integrate/scvi/.config.vsh.yaml b/target/executable/integrate/scvi/.config.vsh.yaml
index 9a3d5f42..3ad5c0f1 100644
--- a/target/executable/integrate/scvi/.config.vsh.yaml
+++ b/target/executable/integrate/scvi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvi"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Malte D. Luecken"
   roles:
@@ -563,7 +563,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -600,11 +600,11 @@ build_info:
   output: "target/executable/integrate/scvi"
   executable: "target/executable/integrate/scvi/scvi"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -634,7 +634,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/integrate/scvi/scvi b/target/executable/integrate/scvi/scvi
index e114ced2..e976e1cf 100755
--- a/target/executable/integrate/scvi/scvi
+++ b/target/executable/integrate/scvi/scvi
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scvi v4.0.0
+# scvi v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Malte D. Luecken, Dries Schaumont, Matthias Beyens"
 LABEL org.opencontainers.image.description="Companion container for running component integrate scvi"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:25Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scvi v4.0.0"
+  echo "scvi v4.0.1"
   echo ""
   echo "Performs scvi integration as done in the human lung cell atlas"
   echo "https://github.com/LungCellAtlas/HLCA"
@@ -856,7 +856,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scvi v4.0.0"
+            echo "scvi v4.0.1"
             exit
             ;;
         --input)
@@ -1349,7 +1349,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scvi:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scvi:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/integrate/totalvi/.config.vsh.yaml b/target/executable/integrate/totalvi/.config.vsh.yaml
index 16f9f1fa..a3dc336c 100644
--- a/target/executable/integrate/totalvi/.config.vsh.yaml
+++ b/target/executable/integrate/totalvi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -484,7 +484,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -517,11 +517,11 @@ build_info:
   output: "target/executable/integrate/totalvi"
   executable: "target/executable/integrate/totalvi/totalvi"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -551,7 +551,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/integrate/totalvi/totalvi b/target/executable/integrate/totalvi/totalvi
index 19bcd2a1..e3ac42b8 100755
--- a/target/executable/integrate/totalvi/totalvi
+++ b/target/executable/integrate/totalvi/totalvi
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# totalvi v4.0.0
+# totalvi v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component integrate totalvi"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:26Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "totalvi v4.0.0"
+  echo "totalvi v4.0.1"
   echo ""
   echo "Performs TotalVI integration of CITE-seq and scRNA-seq data."
   echo ""
@@ -824,7 +824,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "totalvi v4.0.0"
+            echo "totalvi v4.0.1"
             exit
             ;;
         --input)
@@ -1263,7 +1263,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/integrate/totalvi_scarches/.config.vsh.yaml b/target/executable/integrate/totalvi_scarches/.config.vsh.yaml
index 9a400fe0..84b0af30 100644
--- a/target/executable/integrate/totalvi_scarches/.config.vsh.yaml
+++ b/target/executable/integrate/totalvi_scarches/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi_scarches"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   info:
@@ -353,7 +353,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -385,11 +385,11 @@ build_info:
   output: "target/executable/integrate/totalvi_scarches"
   executable: "target/executable/integrate/totalvi_scarches/totalvi_scarches"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -419,7 +419,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/integrate/totalvi_scarches/totalvi_scarches b/target/executable/integrate/totalvi_scarches/totalvi_scarches
index f73ef8c8..f18c0c91 100755
--- a/target/executable/integrate/totalvi_scarches/totalvi_scarches
+++ b/target/executable/integrate/totalvi_scarches/totalvi_scarches
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# totalvi_scarches v4.0.0
+# totalvi_scarches v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component integrate totalvi_scarches"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:25Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "totalvi_scarches v4.0.0"
+  echo "totalvi_scarches v4.0.1"
   echo ""
   echo "Performs totalVI integration by mapping the query dataset to a reference dataset"
   echo "or model."
@@ -745,7 +745,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "totalvi_scarches v4.0.0"
+            echo "totalvi_scarches v4.0.1"
             exit
             ;;
         --input)
@@ -1107,7 +1107,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi_scarches:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi_scarches:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/interpret/lianapy/.config.vsh.yaml b/target/executable/interpret/lianapy/.config.vsh.yaml
index 5432d1c6..d97c2c9b 100644
--- a/target/executable/interpret/lianapy/.config.vsh.yaml
+++ b/target/executable/interpret/lianapy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "lianapy"
 namespace: "interpret"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Mauro Saporita"
   roles:
@@ -320,7 +320,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -357,11 +357,11 @@ build_info:
   output: "target/executable/interpret/lianapy"
   executable: "target/executable/interpret/lianapy/lianapy"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -391,7 +391,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/interpret/lianapy/lianapy b/target/executable/interpret/lianapy/lianapy
index ba1dcfad..536ec3f4 100755
--- a/target/executable/interpret/lianapy/lianapy
+++ b/target/executable/interpret/lianapy/lianapy
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# lianapy v4.0.0
+# lianapy v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Mauro Saporita, Povilas Gibas"
 LABEL org.opencontainers.image.description="Companion container for running component interpret lianapy"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:40Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "lianapy v4.0.0"
+  echo "lianapy v4.0.1"
   echo ""
   echo "Performs LIANA integration based as described in"
   echo "https://github.com/saezlab/liana-py"
@@ -722,7 +722,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "lianapy v4.0.0"
+            echo "lianapy v4.0.1"
             exit
             ;;
         --input)
@@ -996,7 +996,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/interpret/lianapy:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/interpret/lianapy:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/labels_transfer/knn/.config.vsh.yaml b/target/executable/labels_transfer/knn/.config.vsh.yaml
index 80059910..00d6dee5 100644
--- a/target/executable/labels_transfer/knn/.config.vsh.yaml
+++ b/target/executable/labels_transfer/knn/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "knn"
 namespace: "labels_transfer"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -406,7 +406,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -455,11 +455,11 @@ build_info:
   output: "target/executable/labels_transfer/knn"
   executable: "target/executable/labels_transfer/knn/knn"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -489,7 +489,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/labels_transfer/knn/knn b/target/executable/labels_transfer/knn/knn
index 11c77e08..425d5678 100755
--- a/target/executable/labels_transfer/knn/knn
+++ b/target/executable/labels_transfer/knn/knn
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# knn v4.0.0
+# knn v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -462,10 +462,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component labels_transfer knn"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:40Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:20Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -582,7 +582,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "knn v4.0.0"
+  echo "knn v4.0.1"
   echo ""
   echo "This component performs label transfer from reference to query using a K-Neirest"
   echo "Neighbors classifier."
@@ -738,7 +738,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "knn v4.0.0"
+            echo "knn v4.0.1"
             exit
             ;;
         --input)
@@ -1001,7 +1001,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/knn:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/knn:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/labels_transfer/xgboost/.config.vsh.yaml b/target/executable/labels_transfer/xgboost/.config.vsh.yaml
index b94056d8..0d14e4f7 100644
--- a/target/executable/labels_transfer/xgboost/.config.vsh.yaml
+++ b/target/executable/labels_transfer/xgboost/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "xgboost"
 namespace: "labels_transfer"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -555,7 +555,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -604,11 +604,11 @@ build_info:
   output: "target/executable/labels_transfer/xgboost"
   executable: "target/executable/labels_transfer/xgboost/xgboost"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -638,7 +638,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/labels_transfer/xgboost/xgboost b/target/executable/labels_transfer/xgboost/xgboost
index aa0f65f5..83390858 100755
--- a/target/executable/labels_transfer/xgboost/xgboost
+++ b/target/executable/labels_transfer/xgboost/xgboost
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# xgboost v4.0.0
+# xgboost v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -465,10 +465,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component labels_transfer xgboost"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:40Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:20Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "xgboost v4.0.0"
+  echo "xgboost v4.0.1"
   echo ""
   echo "Performs label transfer from reference to query using XGBoost classifier"
   echo ""
@@ -839,7 +839,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "xgboost v4.0.0"
+            echo "xgboost v4.0.1"
             exit
             ;;
         --input)
@@ -1291,7 +1291,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/xgboost:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/xgboost:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/bd_rhapsody/.config.vsh.yaml b/target/executable/mapping/bd_rhapsody/.config.vsh.yaml
index 75aea356..fe2afc14 100644
--- a/target/executable/mapping/bd_rhapsody/.config.vsh.yaml
+++ b/target/executable/mapping/bd_rhapsody/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bd_rhapsody"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -1098,7 +1098,7 @@ engines:
   id: "docker"
   image: "bdgenomics/rhapsody:2.2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -1125,11 +1125,11 @@ build_info:
   output: "target/executable/mapping/bd_rhapsody"
   executable: "target/executable/mapping/bd_rhapsody/bd_rhapsody"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -1159,7 +1159,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/bd_rhapsody/bd_rhapsody b/target/executable/mapping/bd_rhapsody/bd_rhapsody
index 0f7e9abd..772e16fe 100755
--- a/target/executable/mapping/bd_rhapsody/bd_rhapsody
+++ b/target/executable/mapping/bd_rhapsody/bd_rhapsody
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# bd_rhapsody v4.0.0
+# bd_rhapsody v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component mapping bd_rhapsody"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bd_rhapsody v4.0.0"
+  echo "bd_rhapsody v4.0.1"
   echo ""
   echo "BD Rhapsody Sequence Analysis CWL pipeline v2.2.1"
   echo "This pipeline performs analysis of single-cell multiomic sequence read (FASTQ)"
@@ -1113,7 +1113,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "bd_rhapsody v4.0.0"
+            echo "bd_rhapsody v4.0.1"
             exit
             ;;
         --reads)
@@ -1964,7 +1964,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/bd_rhapsody:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/bd_rhapsody:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml b/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml
index ab16f8dd..49e3f2a5 100644
--- a/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml
+++ b/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_atac_count"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -235,7 +235,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger_atac:2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -253,11 +253,11 @@ build_info:
   output: "target/executable/mapping/cellranger_atac_count"
   executable: "target/executable/mapping/cellranger_atac_count/cellranger_atac_count"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -287,7 +287,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/cellranger_atac_count/cellranger_atac_count b/target/executable/mapping/cellranger_atac_count/cellranger_atac_count
index ed8b2bb1..14e5ae92 100755
--- a/target/executable/mapping/cellranger_atac_count/cellranger_atac_count
+++ b/target/executable/mapping/cellranger_atac_count/cellranger_atac_count
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_atac_count v4.0.0
+# cellranger_atac_count v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ RUN DEBIAN_FRONTEND=noninteractive apt update \
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_atac_count"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:31Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_atac_count v4.0.0"
+  echo "cellranger_atac_count v4.0.1"
   echo ""
   echo "Align fastq files using Cell Ranger ATAC count."
   echo ""
@@ -681,7 +681,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_atac_count v4.0.0"
+            echo "cellranger_atac_count v4.0.1"
             exit
             ;;
         --input)
@@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_atac_count:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_atac_count:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/cellranger_count/.config.vsh.yaml b/target/executable/mapping/cellranger_count/.config.vsh.yaml
index a83d6591..c46f6ab3 100644
--- a/target/executable/mapping/cellranger_count/.config.vsh.yaml
+++ b/target/executable/mapping/cellranger_count/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_count"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -367,7 +367,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -397,11 +397,11 @@ build_info:
   output: "target/executable/mapping/cellranger_count"
   executable: "target/executable/mapping/cellranger_count/cellranger_count"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -431,7 +431,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/cellranger_count/cellranger_count b/target/executable/mapping/cellranger_count/cellranger_count
index 811f7d25..b2b7c3e4 100755
--- a/target/executable/mapping/cellranger_count/cellranger_count
+++ b/target/executable/mapping/cellranger_count/cellranger_count
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_count v4.0.0
+# cellranger_count v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_count v4.0.0"
+  echo "cellranger_count v4.0.1"
   echo ""
   echo "Align fastq files using Cell Ranger count."
   echo ""
@@ -747,7 +747,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_count v4.0.0"
+            echo "cellranger_count v4.0.1"
             exit
             ;;
         --input)
@@ -1037,7 +1037,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/cellranger_count_split/.config.vsh.yaml b/target/executable/mapping/cellranger_count_split/.config.vsh.yaml
index 64ad23db..a78ad9cd 100644
--- a/target/executable/mapping/cellranger_count_split/.config.vsh.yaml
+++ b/target/executable/mapping/cellranger_count_split/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_count_split"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -224,7 +224,7 @@ engines:
   id: "docker"
   image: "ubuntu:jammy"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -241,11 +241,11 @@ build_info:
   output: "target/executable/mapping/cellranger_count_split"
   executable: "target/executable/mapping/cellranger_count_split/cellranger_count_split"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -275,7 +275,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/cellranger_count_split/cellranger_count_split b/target/executable/mapping/cellranger_count_split/cellranger_count_split
index c75e899c..e77bc8b5 100755
--- a/target/executable/mapping/cellranger_count_split/cellranger_count_split
+++ b/target/executable/mapping/cellranger_count_split/cellranger_count_split
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_count_split v4.0.0
+# cellranger_count_split v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ ENTRYPOINT []
 RUN apt update && apt upgrade -y
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count_split"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_count_split v4.0.0"
+  echo "cellranger_count_split v4.0.1"
   echo ""
   echo "Split 10x Cell Ranger output directory into separate output fields."
   echo ""
@@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_count_split v4.0.0"
+            echo "cellranger_count_split v4.0.1"
             exit
             ;;
         --input)
@@ -828,7 +828,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count_split:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count_split:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/cellranger_multi/.config.vsh.yaml b/target/executable/mapping/cellranger_multi/.config.vsh.yaml
index bd6933a4..b20af07d 100644
--- a/target/executable/mapping/cellranger_multi/.config.vsh.yaml
+++ b/target/executable/mapping/cellranger_multi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_multi"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -952,7 +952,7 @@ engines:
   id: "docker"
   image: "quay.io/nf-core/cellranger:10.0.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -991,11 +991,11 @@ build_info:
   output: "target/executable/mapping/cellranger_multi"
   executable: "target/executable/mapping/cellranger_multi/cellranger_multi"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -1025,7 +1025,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/cellranger_multi/cellranger_multi b/target/executable/mapping/cellranger_multi/cellranger_multi
index 1873cce1..ddb2852a 100755
--- a/target/executable/mapping/cellranger_multi/cellranger_multi
+++ b/target/executable/mapping/cellranger_multi/cellranger_multi
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_multi v4.0.0
+# cellranger_multi v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -463,10 +463,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer, Weiwei Schultz, Dorien Roosen"
 LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_multi"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:31Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -583,7 +583,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_multi v4.0.0"
+  echo "cellranger_multi v4.0.1"
   echo ""
   echo "Align fastq files using Cell Ranger multi."
   echo ""
@@ -1133,7 +1133,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_multi v4.0.0"
+            echo "cellranger_multi v4.0.1"
             exit
             ;;
         --input)
@@ -1983,7 +1983,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_multi:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_multi:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/htseq_count/.config.vsh.yaml b/target/executable/mapping/htseq_count/.config.vsh.yaml
index e7b166f0..376c671e 100644
--- a/target/executable/mapping/htseq_count/.config.vsh.yaml
+++ b/target/executable/mapping/htseq_count/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "htseq_count"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -396,7 +396,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -422,11 +422,11 @@ build_info:
   output: "target/executable/mapping/htseq_count"
   executable: "target/executable/mapping/htseq_count/htseq_count"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -456,7 +456,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/htseq_count/htseq_count b/target/executable/mapping/htseq_count/htseq_count
index ee99d6fb..4c15cc45 100755
--- a/target/executable/mapping/htseq_count/htseq_count
+++ b/target/executable/mapping/htseq_count/htseq_count
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# htseq_count v4.0.0
+# htseq_count v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco"
 LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "htseq_count v4.0.0"
+  echo "htseq_count v4.0.1"
   echo ""
   echo "Quantify gene expression for subsequent testing for differential expression."
   echo ""
@@ -762,7 +762,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "htseq_count v4.0.0"
+            echo "htseq_count v4.0.1"
             exit
             ;;
         --input)
@@ -1102,7 +1102,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml
index 1a335f4e..e07c182a 100644
--- a/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml
+++ b/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "htseq_count_to_h5mu"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -201,7 +201,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -236,11 +236,11 @@ build_info:
   output: "target/executable/mapping/htseq_count_to_h5mu"
   executable: "target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -270,7 +270,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu b/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu
index 29a50485..d994bbd6 100755
--- a/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu
+++ b/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# htseq_count_to_h5mu v4.0.0
+# htseq_count_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -462,10 +462,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco"
 LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:31Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -582,7 +582,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "htseq_count_to_h5mu v4.0.0"
+  echo "htseq_count_to_h5mu v4.0.1"
   echo ""
   echo "Convert the htseq table to a h5mu."
   echo ""
@@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "htseq_count_to_h5mu v4.0.0"
+            echo "htseq_count_to_h5mu v4.0.1"
             exit
             ;;
         --input_id)
@@ -826,7 +826,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/multi_star/.config.vsh.yaml b/target/executable/mapping/multi_star/.config.vsh.yaml
index 1af5ce9d..32f30019 100644
--- a/target/executable/mapping/multi_star/.config.vsh.yaml
+++ b/target/executable/mapping/multi_star/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "multi_star"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -2856,7 +2856,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -2904,11 +2904,11 @@ build_info:
   output: "target/executable/mapping/multi_star"
   executable: "target/executable/mapping/multi_star/multi_star"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -2938,7 +2938,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/multi_star/multi_star b/target/executable/mapping/multi_star/multi_star
index 4f0c5b29..1a6c382e 100755
--- a/target/executable/mapping/multi_star/multi_star
+++ b/target/executable/mapping/multi_star/multi_star
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# multi_star v4.0.0
+# multi_star v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -473,10 +473,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -593,7 +593,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "multi_star v4.0.0"
+  echo "multi_star v4.0.1"
   echo ""
   echo "Align fastq files using STAR."
   echo ""
@@ -2097,7 +2097,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "multi_star v4.0.0"
+            echo "multi_star v4.0.1"
             exit
             ;;
         --input_id)
@@ -4637,7 +4637,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml
index 2fd6578f..f83caec6 100644
--- a/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml
+++ b/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "multi_star_to_h5mu"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -177,7 +177,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -206,11 +206,11 @@ build_info:
   output: "target/executable/mapping/multi_star_to_h5mu"
   executable: "target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -240,7 +240,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu b/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu
index 282bffd2..af8bcdea 100755
--- a/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu
+++ b/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# multi_star_to_h5mu v4.0.0
+# multi_star_to_h5mu v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco"
 LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star_to_h5mu"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:33Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "multi_star_to_h5mu v4.0.0"
+  echo "multi_star_to_h5mu v4.0.1"
   echo ""
   echo "Convert the output of \`multi_star\` to a h5mu."
   echo ""
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "multi_star_to_h5mu v4.0.0"
+            echo "multi_star_to_h5mu v4.0.1"
             exit
             ;;
         --input)
@@ -778,7 +778,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star_to_h5mu:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star_to_h5mu:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/samtools_sort/.config.vsh.yaml b/target/executable/mapping/samtools_sort/.config.vsh.yaml
index cc0213d0..0b8a13b0 100644
--- a/target/executable/mapping/samtools_sort/.config.vsh.yaml
+++ b/target/executable/mapping/samtools_sort/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools_sort"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -258,7 +258,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -282,11 +282,11 @@ build_info:
   output: "target/executable/mapping/samtools_sort"
   executable: "target/executable/mapping/samtools_sort/samtools_sort"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -316,7 +316,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/samtools_sort/samtools_sort b/target/executable/mapping/samtools_sort/samtools_sort
index 13f65ebd..c22d69cf 100755
--- a/target/executable/mapping/samtools_sort/samtools_sort
+++ b/target/executable/mapping/samtools_sort/samtools_sort
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# samtools_sort v4.0.0
+# samtools_sort v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco"
 LABEL org.opencontainers.image.description="Companion container for running component mapping samtools_sort"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:33Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "samtools_sort v4.0.0"
+  echo "samtools_sort v4.0.1"
   echo ""
   echo "Sort and (optionally) index alignments."
   echo ""
@@ -702,7 +702,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "samtools_sort v4.0.0"
+            echo "samtools_sort v4.0.1"
             exit
             ;;
         --input)
@@ -885,7 +885,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/samtools_sort:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/samtools_sort:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/star_align/.config.vsh.yaml b/target/executable/mapping/star_align/.config.vsh.yaml
index b20cc70f..cb90395a 100644
--- a/target/executable/mapping/star_align/.config.vsh.yaml
+++ b/target/executable/mapping/star_align/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "star_align"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -2341,7 +2341,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -2371,11 +2371,11 @@ build_info:
   output: "target/executable/mapping/star_align"
   executable: "target/executable/mapping/star_align/star_align"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -2405,7 +2405,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/star_align/star_align b/target/executable/mapping/star_align/star_align
index 9ec976f9..65d632fc 100755
--- a/target/executable/mapping/star_align/star_align
+++ b/target/executable/mapping/star_align/star_align
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# star_align v4.0.0
+# star_align v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -470,10 +470,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component mapping star_align"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -590,7 +590,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "star_align v4.0.0"
+  echo "star_align v4.0.1"
   echo ""
   echo "Align fastq files using STAR."
   echo ""
@@ -2025,7 +2025,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "star_align v4.0.0"
+            echo "star_align v4.0.1"
             exit
             ;;
         --input)
@@ -4415,7 +4415,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/mapping/star_align_v273a/.config.vsh.yaml b/target/executable/mapping/star_align_v273a/.config.vsh.yaml
index 33ede43f..e1528c89 100644
--- a/target/executable/mapping/star_align_v273a/.config.vsh.yaml
+++ b/target/executable/mapping/star_align_v273a/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "star_align_v273a"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -2341,7 +2341,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -2371,11 +2371,11 @@ build_info:
   output: "target/executable/mapping/star_align_v273a"
   executable: "target/executable/mapping/star_align_v273a/star_align_v273a"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -2405,7 +2405,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/mapping/star_align_v273a/star_align_v273a b/target/executable/mapping/star_align_v273a/star_align_v273a
index 5d416ecf..e85782b7 100755
--- a/target/executable/mapping/star_align_v273a/star_align_v273a
+++ b/target/executable/mapping/star_align_v273a/star_align_v273a
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# star_align_v273a v4.0.0
+# star_align_v273a v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -470,10 +470,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component mapping star_align_v273a"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:33Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -590,7 +590,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "star_align_v273a v4.0.0"
+  echo "star_align_v273a v4.0.1"
   echo ""
   echo "Align fastq files using STAR."
   echo ""
@@ -2025,7 +2025,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "star_align_v273a v4.0.0"
+            echo "star_align_v273a v4.0.1"
             exit
             ;;
         --input)
@@ -4415,7 +4415,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align_v273a:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align_v273a:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/metadata/add_id/.config.vsh.yaml b/target/executable/metadata/add_id/.config.vsh.yaml
index d2ed07c7..0f9a97d5 100644
--- a/target/executable/metadata/add_id/.config.vsh.yaml
+++ b/target/executable/metadata/add_id/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "add_id"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -185,7 +185,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -226,11 +226,11 @@ build_info:
   output: "target/executable/metadata/add_id"
   executable: "target/executable/metadata/add_id/add_id"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -260,7 +260,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/metadata/add_id/add_id b/target/executable/metadata/add_id/add_id
index 99a50fe7..5bbd7d36 100755
--- a/target/executable/metadata/add_id/add_id
+++ b/target/executable/metadata/add_id/add_id
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# add_id v4.0.0
+# add_id v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component metadata add_id"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "add_id v4.0.0"
+  echo "add_id v4.0.1"
   echo ""
   echo "Add id of .obs. Also allows to make .obs_names (the .obs index) unique"
   echo "by prefixing the values with an unique id per .h5mu file."
@@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "add_id v4.0.0"
+            echo "add_id v4.0.1"
             exit
             ;;
         --input)
@@ -824,7 +824,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/add_id:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/add_id:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/metadata/grep_annotation_column/.config.vsh.yaml b/target/executable/metadata/grep_annotation_column/.config.vsh.yaml
index 6cec3c32..5127ae71 100644
--- a/target/executable/metadata/grep_annotation_column/.config.vsh.yaml
+++ b/target/executable/metadata/grep_annotation_column/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "grep_annotation_column"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -241,7 +241,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -282,11 +282,11 @@ build_info:
   output: "target/executable/metadata/grep_annotation_column"
   executable: "target/executable/metadata/grep_annotation_column/grep_annotation_column"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -316,7 +316,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/metadata/grep_annotation_column/grep_annotation_column b/target/executable/metadata/grep_annotation_column/grep_annotation_column
index eece3ed1..e8fa0959 100755
--- a/target/executable/metadata/grep_annotation_column/grep_annotation_column
+++ b/target/executable/metadata/grep_annotation_column/grep_annotation_column
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# grep_annotation_column v4.0.0
+# grep_annotation_column v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component metadata grep_annotation_column"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:40Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "grep_annotation_column v4.0.0"
+  echo "grep_annotation_column v4.0.1"
   echo ""
   echo "Perform a regex lookup on a column from the annotation matrices .obs or .var."
   echo "The annotation matrix can originate from either a modality, or all modalities"
@@ -694,7 +694,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "grep_annotation_column v4.0.0"
+            echo "grep_annotation_column v4.0.1"
             exit
             ;;
         --input)
@@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/grep_annotation_column:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/grep_annotation_column:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/metadata/join_csv/.config.vsh.yaml b/target/executable/metadata/join_csv/.config.vsh.yaml
index 10605b96..32e01732 100644
--- a/target/executable/metadata/join_csv/.config.vsh.yaml
+++ b/target/executable/metadata/join_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "join_csv"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -216,7 +216,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -257,11 +257,11 @@ build_info:
   output: "target/executable/metadata/join_csv"
   executable: "target/executable/metadata/join_csv/join_csv"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -291,7 +291,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/metadata/join_csv/join_csv b/target/executable/metadata/join_csv/join_csv
index 0662bdfc..8e3e457d 100755
--- a/target/executable/metadata/join_csv/join_csv
+++ b/target/executable/metadata/join_csv/join_csv
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# join_csv v4.0.0
+# join_csv v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component metadata join_csv"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:40Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "join_csv v4.0.0"
+  echo "join_csv v4.0.1"
   echo ""
   echo "Join a csv containing metadata to the .obs or .var field of a mudata file."
   echo ""
@@ -676,7 +676,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "join_csv v4.0.0"
+            echo "join_csv v4.0.1"
             exit
             ;;
         --input)
@@ -867,7 +867,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_csv:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_csv:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml b/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml
index 50a7f9c0..ad948f7e 100644
--- a/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml
+++ b/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "join_uns_to_obs"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -164,7 +164,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -205,11 +205,11 @@ build_info:
   output: "target/executable/metadata/join_uns_to_obs"
   executable: "target/executable/metadata/join_uns_to_obs/join_uns_to_obs"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -239,7 +239,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/metadata/join_uns_to_obs/join_uns_to_obs b/target/executable/metadata/join_uns_to_obs/join_uns_to_obs
index 851c99d3..1c31c939 100755
--- a/target/executable/metadata/join_uns_to_obs/join_uns_to_obs
+++ b/target/executable/metadata/join_uns_to_obs/join_uns_to_obs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# join_uns_to_obs v4.0.0
+# join_uns_to_obs v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
   python -c 'exec("try:\n  import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  assert int(version(\"zarr\").partition(\".\")[0]) > 2")'
 
 LABEL org.opencontainers.image.description="Companion container for running component metadata join_uns_to_obs"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "join_uns_to_obs v4.0.0"
+  echo "join_uns_to_obs v4.0.1"
   echo ""
   echo "Join a data frame of length 1 (1 row index value) in .uns containing metadata to"
   echo "the .obs of a mudata file."
@@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "join_uns_to_obs v4.0.0"
+            echo "join_uns_to_obs v4.0.1"
             exit
             ;;
         --input)
@@ -810,7 +810,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_uns_to_obs:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_uns_to_obs:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml
index 1342832d..18047ed1 100644
--- a/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml
+++ b/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_obsm_to_obs"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -183,7 +183,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -224,11 +224,11 @@ build_info:
   output: "target/executable/metadata/move_obsm_to_obs"
   executable: "target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -258,7 +258,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs b/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs
index b41e35ad..26bd0b50 100755
--- a/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs
+++ b/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# move_obsm_to_obs v4.0.0
+# move_obsm_to_obs v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component metadata move_obsm_to_obs"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "move_obsm_to_obs v4.0.0"
+  echo "move_obsm_to_obs v4.0.1"
   echo ""
   echo "Move a matrix from .obsm to .obs. Newly created columns in .obs will"
   echo "be created from the .obsm key suffixed with an underscore and the name of the"
@@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "move_obsm_to_obs v4.0.0"
+            echo "move_obsm_to_obs v4.0.1"
             exit
             ;;
         --input)
@@ -818,7 +818,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/move_obsm_to_obs:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/move_obsm_to_obs:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/neighbors/bbknn/.config.vsh.yaml b/target/executable/neighbors/bbknn/.config.vsh.yaml
index 295d35a6..25195ee3 100644
--- a/target/executable/neighbors/bbknn/.config.vsh.yaml
+++ b/target/executable/neighbors/bbknn/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bbknn"
 namespace: "neighbors"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -272,7 +272,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -310,11 +310,11 @@ build_info:
   output: "target/executable/neighbors/bbknn"
   executable: "target/executable/neighbors/bbknn/bbknn"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -344,7 +344,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/neighbors/bbknn/bbknn b/target/executable/neighbors/bbknn/bbknn
index 89f3c7a8..7a952bcd 100755
--- a/target/executable/neighbors/bbknn/bbknn
+++ b/target/executable/neighbors/bbknn/bbknn
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# bbknn v4.0.0
+# bbknn v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component neighbors bbknn"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bbknn v4.0.0"
+  echo "bbknn v4.0.1"
   echo ""
   echo "BBKNN network generation"
   echo ""
@@ -702,7 +702,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "bbknn v4.0.0"
+            echo "bbknn v4.0.1"
             exit
             ;;
         --input)
@@ -937,7 +937,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/bbknn:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/bbknn:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/neighbors/find_neighbors/.config.vsh.yaml b/target/executable/neighbors/find_neighbors/.config.vsh.yaml
index 67e74a93..ad9e08e9 100644
--- a/target/executable/neighbors/find_neighbors/.config.vsh.yaml
+++ b/target/executable/neighbors/find_neighbors/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "find_neighbors"
 namespace: "neighbors"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -296,7 +296,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -338,11 +338,11 @@ build_info:
   output: "target/executable/neighbors/find_neighbors"
   executable: "target/executable/neighbors/find_neighbors/find_neighbors"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -372,7 +372,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/neighbors/find_neighbors/find_neighbors b/target/executable/neighbors/find_neighbors/find_neighbors
index e76e8502..c6c2ca08 100755
--- a/target/executable/neighbors/find_neighbors/find_neighbors
+++ b/target/executable/neighbors/find_neighbors/find_neighbors
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# find_neighbors v4.0.0
+# find_neighbors v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component neighbors find_neighbors"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:20Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "find_neighbors v4.0.0"
+  echo "find_neighbors v4.0.1"
   echo ""
   echo "Compute a neighborhood graph of observations [McInnes18]."
   echo ""
@@ -707,7 +707,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "find_neighbors v4.0.0"
+            echo "find_neighbors v4.0.1"
             exit
             ;;
         --input)
@@ -931,7 +931,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/find_neighbors:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/find_neighbors:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml
index a15ea68b..c2ea4324 100644
--- a/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml
+++ b/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_10xh5"
 namespace: "process_10xh5"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -182,7 +182,7 @@ engines:
   id: "docker"
   image: "eddelbuettel/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -226,11 +226,11 @@ build_info:
   output: "target/executable/process_10xh5/filter_10xh5"
   executable: "target/executable/process_10xh5/filter_10xh5/filter_10xh5"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -260,7 +260,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/process_10xh5/filter_10xh5/filter_10xh5 b/target/executable/process_10xh5/filter_10xh5/filter_10xh5
index d491c018..d206378a 100755
--- a/target/executable/process_10xh5/filter_10xh5/filter_10xh5
+++ b/target/executable/process_10xh5/filter_10xh5/filter_10xh5
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# filter_10xh5 v4.0.0
+# filter_10xh5 v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -463,10 +463,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component process_10xh5 filter_10xh5"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:38Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -583,7 +583,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "filter_10xh5 v4.0.0"
+  echo "filter_10xh5 v4.0.1"
   echo ""
   echo "Filter a 10x h5 dataset."
   echo ""
@@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "filter_10xh5 v4.0.0"
+            echo "filter_10xh5 v4.0.1"
             exit
             ;;
         --input)
@@ -827,7 +827,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/process_10xh5/filter_10xh5:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/process_10xh5/filter_10xh5:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml b/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml
index 6a8f88d9..9f64db0d 100644
--- a/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml
+++ b/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "calculate_atac_qc_metrics"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -249,7 +249,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -283,11 +283,11 @@ build_info:
   output: "target/executable/qc/calculate_atac_qc_metrics"
   executable: "target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -317,7 +317,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics b/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics
index 14ea36a3..4255b3d6 100755
--- a/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics
+++ b/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# calculate_atac_qc_metrics v4.0.0
+# calculate_atac_qc_metrics v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component qc calculate_atac_qc_metrics"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "calculate_atac_qc_metrics v4.0.0"
+  echo "calculate_atac_qc_metrics v4.0.1"
   echo ""
   echo "Add basic ATAC quality control metrics to an .h5mu file."
   echo ""
@@ -709,7 +709,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "calculate_atac_qc_metrics v4.0.0"
+            echo "calculate_atac_qc_metrics v4.0.1"
             exit
             ;;
         --input)
@@ -910,7 +910,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_atac_qc_metrics:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_atac_qc_metrics:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml b/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml
index f8e6d635..ff10d909 100644
--- a/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml
+++ b/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "calculate_qc_metrics"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -295,7 +295,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -342,11 +342,11 @@ build_info:
   output: "target/executable/qc/calculate_qc_metrics"
   executable: "target/executable/qc/calculate_qc_metrics/calculate_qc_metrics"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -376,7 +376,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics b/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics
index 0cb78152..db5d24b7 100755
--- a/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics
+++ b/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# calculate_qc_metrics v4.0.0
+# calculate_qc_metrics v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component qc calculate_qc_metrics"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "calculate_qc_metrics v4.0.0"
+  echo "calculate_qc_metrics v4.0.1"
   echo ""
   echo "Add basic quality control metrics to an .h5mu file."
   echo ""
@@ -742,7 +742,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "calculate_qc_metrics v4.0.0"
+            echo "calculate_qc_metrics v4.0.1"
             exit
             ;;
         --input)
@@ -999,7 +999,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_qc_metrics:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_qc_metrics:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/qc/fastqc/.config.vsh.yaml b/target/executable/qc/fastqc/.config.vsh.yaml
index 450e540e..7f3e8eab 100644
--- a/target/executable/qc/fastqc/.config.vsh.yaml
+++ b/target/executable/qc/fastqc/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "fastqc"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -158,7 +158,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -176,11 +176,11 @@ build_info:
   output: "target/executable/qc/fastqc"
   executable: "target/executable/qc/fastqc/fastqc"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -210,7 +210,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/qc/fastqc/fastqc b/target/executable/qc/fastqc/fastqc
index eee0d632..f38e4abe 100755
--- a/target/executable/qc/fastqc/fastqc
+++ b/target/executable/qc/fastqc/fastqc
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# fastqc v4.0.0
+# fastqc v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component qc fastqc"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:40Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "fastqc v4.0.0"
+  echo "fastqc v4.0.1"
   echo ""
   echo "Fastqc component, please see"
   echo "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can"
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "fastqc v4.0.0"
+            echo "fastqc v4.0.1"
             exit
             ;;
         --mode)
@@ -805,7 +805,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/fastqc:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/fastqc:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/qc/multiqc/.config.vsh.yaml b/target/executable/qc/multiqc/.config.vsh.yaml
index e2922eb8..6be2b165 100644
--- a/target/executable/qc/multiqc/.config.vsh.yaml
+++ b/target/executable/qc/multiqc/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "multiqc"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -133,7 +133,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -162,11 +162,11 @@ build_info:
   output: "target/executable/qc/multiqc"
   executable: "target/executable/qc/multiqc/multiqc"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -196,7 +196,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/qc/multiqc/multiqc b/target/executable/qc/multiqc/multiqc
index 9dcb368f..ec494eb7 100755
--- a/target/executable/qc/multiqc/multiqc
+++ b/target/executable/qc/multiqc/multiqc
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# multiqc v4.0.0
+# multiqc v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "multiqc"
 
 LABEL org.opencontainers.image.description="Companion container for running component qc multiqc"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "multiqc v4.0.0"
+  echo "multiqc v4.0.1"
   echo ""
   echo "MultiQC aggregates results from bioinformatics analyses across many samples into"
   echo "a single report."
@@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "multiqc v4.0.0"
+            echo "multiqc v4.0.1"
             exit
             ;;
         --input)
@@ -773,7 +773,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/multiqc:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/multiqc:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/query/cellxgene_census/.config.vsh.yaml b/target/executable/query/cellxgene_census/.config.vsh.yaml
index a217bbe0..e1fc312c 100644
--- a/target/executable/query/cellxgene_census/.config.vsh.yaml
+++ b/target/executable/query/cellxgene_census/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellxgene_census"
 namespace: "query"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Matthias Beyens"
   roles:
@@ -506,7 +506,7 @@ engines:
   id: "docker"
   image: "python:3.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -539,11 +539,11 @@ build_info:
   output: "target/executable/query/cellxgene_census"
   executable: "target/executable/query/cellxgene_census/cellxgene_census"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -573,7 +573,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/query/cellxgene_census/cellxgene_census b/target/executable/query/cellxgene_census/cellxgene_census
index b5eb407f..0e8e0e30 100755
--- a/target/executable/query/cellxgene_census/cellxgene_census
+++ b/target/executable/query/cellxgene_census/cellxgene_census
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellxgene_census v4.0.0
+# cellxgene_census v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Matthias Beyens, Dries De Maeyer, Robrecht Cannoodt, Kai Waldrant"
 LABEL org.opencontainers.image.description="Companion container for running component query cellxgene_census"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:29Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellxgene_census v4.0.0"
+  echo "cellxgene_census v4.0.1"
   echo ""
   echo "Query cells from a CellxGene Census or custom TileDBSoma object."
   echo "Aside from fetching the cells' RNA counts (\`.X\`), cell metadata"
@@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellxgene_census v4.0.0"
+            echo "cellxgene_census v4.0.1"
             exit
             ;;
         --input_uri)
@@ -992,7 +992,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/cellxgene_census:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/cellxgene_census:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/query/tiledb_healthcheck/.config.vsh.yaml b/target/executable/query/tiledb_healthcheck/.config.vsh.yaml
index 73b018c0..dad438fc 100644
--- a/target/executable/query/tiledb_healthcheck/.config.vsh.yaml
+++ b/target/executable/query/tiledb_healthcheck/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tiledb_healthcheck"
 namespace: "query"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -137,7 +137,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -162,11 +162,11 @@ build_info:
   output: "target/executable/query/tiledb_healthcheck"
   executable: "target/executable/query/tiledb_healthcheck/tiledb_healthcheck"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -196,7 +196,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/query/tiledb_healthcheck/tiledb_healthcheck b/target/executable/query/tiledb_healthcheck/tiledb_healthcheck
index e05da8a6..3fbfed73 100755
--- a/target/executable/query/tiledb_healthcheck/tiledb_healthcheck
+++ b/target/executable/query/tiledb_healthcheck/tiledb_healthcheck
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# tiledb_healthcheck v4.0.0
+# tiledb_healthcheck v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component query tiledb_healthcheck"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:29Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "tiledb_healthcheck v4.0.0"
+  echo "tiledb_healthcheck v4.0.1"
   echo ""
   echo "Checks if a provided location can be queried as a TileDB-SOMA database."
   echo ""
@@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "tiledb_healthcheck v4.0.0"
+            echo "tiledb_healthcheck v4.0.1"
             exit
             ;;
         --input_uri)
@@ -749,7 +749,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/tiledb_healthcheck:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/tiledb_healthcheck:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml b/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml
index 2c2120de..bf116f83 100644
--- a/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml
+++ b/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_bdrhap_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -249,7 +249,7 @@ engines:
   id: "docker"
   image: "bdgenomics/rhapsody:2.2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -274,11 +274,11 @@ build_info:
   output: "target/executable/reference/build_bdrhap_reference"
   executable: "target/executable/reference/build_bdrhap_reference/build_bdrhap_reference"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -308,7 +308,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference b/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference
index 3109c4ef..0a773fc0 100755
--- a/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference
+++ b/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# build_bdrhap_reference v4.0.0
+# build_bdrhap_reference v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component reference build_bdrhap_reference"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "build_bdrhap_reference v4.0.0"
+  echo "build_bdrhap_reference v4.0.1"
   echo ""
   echo "The Reference Files Generator creates an archive containing Genome Index"
   echo "and Transcriptome annotation files needed for the BD Rhapsody Sequencing"
@@ -711,7 +711,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "build_bdrhap_reference v4.0.0"
+            echo "build_bdrhap_reference v4.0.1"
             exit
             ;;
         --genome_fasta)
@@ -902,7 +902,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_bdrhap_reference:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_bdrhap_reference:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml b/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml
index b0b3472d..a5d47eeb 100644
--- a/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml
+++ b/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_cellranger_arc_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -213,7 +213,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger_arc:2.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -246,11 +246,11 @@ build_info:
   output: "target/executable/reference/build_cellranger_arc_reference"
   executable: "target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference b/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference
index 24540eef..23581b75 100755
--- a/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference
+++ b/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# build_cellranger_arc_reference v4.0.0
+# build_cellranger_arc_reference v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ apt upgrade -y && apt install -y procps pigz && rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component reference build_cellranger_arc_reference"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:45Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "build_cellranger_arc_reference v4.0.0"
+  echo "build_cellranger_arc_reference v4.0.1"
   echo ""
   echo "Build a Cell Ranger-arc and -atac compatible reference folder from user-supplied"
   echo "genome FASTA and gene GTF files. Creates a new folder named after the genome."
@@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "build_cellranger_arc_reference v4.0.0"
+            echo "build_cellranger_arc_reference v4.0.1"
             exit
             ;;
         --genome_fasta)
@@ -859,7 +859,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_arc_reference:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_arc_reference:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/reference/build_cellranger_reference/.config.vsh.yaml b/target/executable/reference/build_cellranger_reference/.config.vsh.yaml
index 6627a037..183d3ec5 100644
--- a/target/executable/reference/build_cellranger_reference/.config.vsh.yaml
+++ b/target/executable/reference/build_cellranger_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_cellranger_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -182,7 +182,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -214,11 +214,11 @@ build_info:
   output: "target/executable/reference/build_cellranger_reference"
   executable: "target/executable/reference/build_cellranger_reference/build_cellranger_reference"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/reference/build_cellranger_reference/build_cellranger_reference b/target/executable/reference/build_cellranger_reference/build_cellranger_reference
index 4d9d572c..4414a9e6 100755
--- a/target/executable/reference/build_cellranger_reference/build_cellranger_reference
+++ b/target/executable/reference/build_cellranger_reference/build_cellranger_reference
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# build_cellranger_reference v4.0.0
+# build_cellranger_reference v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ apt upgrade -y && apt install -y procps pigz && rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component reference build_cellranger_reference"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:43Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "build_cellranger_reference v4.0.0"
+  echo "build_cellranger_reference v4.0.1"
   echo ""
   echo "Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA"
   echo "and gene GTF files. Creates a new folder named after the genome."
@@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "build_cellranger_reference v4.0.0"
+            echo "build_cellranger_reference v4.0.1"
             exit
             ;;
         --genome_fasta)
@@ -781,7 +781,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_reference:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_reference:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/reference/build_star_reference/.config.vsh.yaml b/target/executable/reference/build_star_reference/.config.vsh.yaml
index 07c59f3b..61cd54de 100644
--- a/target/executable/reference/build_star_reference/.config.vsh.yaml
+++ b/target/executable/reference/build_star_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_star_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -208,11 +208,11 @@ build_info:
   output: "target/executable/reference/build_star_reference"
   executable: "target/executable/reference/build_star_reference/build_star_reference"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -242,7 +242,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/reference/build_star_reference/build_star_reference b/target/executable/reference/build_star_reference/build_star_reference
index a1fa2874..46ccf74a 100755
--- a/target/executable/reference/build_star_reference/build_star_reference
+++ b/target/executable/reference/build_star_reference/build_star_reference
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# build_star_reference v4.0.0
+# build_star_reference v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -469,10 +469,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component reference build_star_reference"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -589,7 +589,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "build_star_reference v4.0.0"
+  echo "build_star_reference v4.0.1"
   echo ""
   echo "Create a reference for STAR from a set of fasta files."
   echo ""
@@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "build_star_reference v4.0.0"
+            echo "build_star_reference v4.0.1"
             exit
             ;;
         --genome_fasta)
@@ -835,7 +835,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_star_reference:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_star_reference:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml b/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml
index ecae7c46..04f46f20 100644
--- a/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml
+++ b/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_mkgtf"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -152,7 +152,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -182,11 +182,11 @@ build_info:
   output: "target/executable/reference/cellranger_mkgtf"
   executable: "target/executable/reference/cellranger_mkgtf/cellranger_mkgtf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -216,7 +216,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf b/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf
index 21af85c1..b22b257b 100755
--- a/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf
+++ b/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# cellranger_mkgtf v4.0.0
+# cellranger_mkgtf v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ apt upgrade -y && apt install -y pigz procps && rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.authors="Jakub Majercik"
 LABEL org.opencontainers.image.description="Companion container for running component reference cellranger_mkgtf"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cellranger_mkgtf v4.0.0"
+  echo "cellranger_mkgtf v4.0.1"
   echo ""
   echo "Make a GTF file - filter by a specific attribute."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "cellranger_mkgtf v4.0.0"
+            echo "cellranger_mkgtf v4.0.1"
             exit
             ;;
         --input_gtf)
@@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/cellranger_mkgtf:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/cellranger_mkgtf:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/reference/make_reference/.config.vsh.yaml b/target/executable/reference/make_reference/.config.vsh.yaml
index b1d1c3eb..8ff85d50 100644
--- a/target/executable/reference/make_reference/.config.vsh.yaml
+++ b/target/executable/reference/make_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "make_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -208,7 +208,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -231,11 +231,11 @@ build_info:
   output: "target/executable/reference/make_reference"
   executable: "target/executable/reference/make_reference/make_reference"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -265,7 +265,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/reference/make_reference/make_reference b/target/executable/reference/make_reference/make_reference
index c1c43725..b716e3dd 100755
--- a/target/executable/reference/make_reference/make_reference
+++ b/target/executable/reference/make_reference/make_reference
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# make_reference v4.0.0
+# make_reference v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component reference make_reference"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "make_reference v4.0.0"
+  echo "make_reference v4.0.1"
   echo ""
   echo "Preprocess and build a transcriptome reference."
   echo ""
@@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "make_reference v4.0.0"
+            echo "make_reference v4.0.1"
             exit
             ;;
         --genome_fasta)
@@ -821,7 +821,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/make_reference:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/make_reference:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/report/mermaid/.config.vsh.yaml b/target/executable/report/mermaid/.config.vsh.yaml
index 1777d1c1..6fadeb13 100644
--- a/target/executable/report/mermaid/.config.vsh.yaml
+++ b/target/executable/report/mermaid/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "mermaid"
 namespace: "report"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -182,7 +182,7 @@ engines:
   id: "docker"
   image: "node:20-bullseye"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "javascript"
@@ -203,11 +203,11 @@ build_info:
   output: "target/executable/report/mermaid"
   executable: "target/executable/report/mermaid/mermaid"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -237,7 +237,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/report/mermaid/mermaid b/target/executable/report/mermaid/mermaid
index ff58a5bd..d70ec223 100755
--- a/target/executable/report/mermaid/mermaid
+++ b/target/executable/report/mermaid/mermaid
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# mermaid v4.0.0
+# mermaid v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -456,10 +456,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer"
 LABEL org.opencontainers.image.description="Companion container for running component report mermaid"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:39Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "mermaid v4.0.0"
+  echo "mermaid v4.0.1"
   echo ""
   echo "Generates a network from mermaid code."
   echo ""
@@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "mermaid v4.0.0"
+            echo "mermaid v4.0.1"
             exit
             ;;
         --input)
@@ -828,7 +828,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/report/mermaid:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/report/mermaid:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml
index a22252c9..adf496d7 100644
--- a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml
+++ b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "assert_test_workflow_2_output"
 namespace: "test_workflows/multiomics/process_samples"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   info:
@@ -136,7 +136,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -169,11 +169,11 @@ build_info:
   output: "target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output"
   executable: "target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -203,7 +203,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output
index 51638bc5..f9796933 100755
--- a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output
+++ b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# assert_test_workflow_2_output v4.0.0
+# assert_test_workflow_2_output v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics/process_samples assert_test_workflow_2_output"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:44Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "assert_test_workflow_2_output v4.0.0"
+  echo "assert_test_workflow_2_output v4.0.1"
   echo ""
   echo "This component tests the output of the integration test of process_samples"
   echo "test_wf."
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "assert_test_workflow_2_output v4.0.0"
+            echo "assert_test_workflow_2_output v4.0.1"
             exit
             ;;
         --input)
@@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_samples/assert_test_workflow_2_output:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_samples/assert_test_workflow_2_output:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/bpcells_regress_out/.config.vsh.yaml b/target/executable/transform/bpcells_regress_out/.config.vsh.yaml
index 5fe973a1..2920f1b7 100644
--- a/target/executable/transform/bpcells_regress_out/.config.vsh.yaml
+++ b/target/executable/transform/bpcells_regress_out/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bpcells_regress_out"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -224,7 +224,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -284,11 +284,11 @@ build_info:
   output: "target/executable/transform/bpcells_regress_out"
   executable: "target/executable/transform/bpcells_regress_out/bpcells_regress_out"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -318,7 +318,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/bpcells_regress_out/bpcells_regress_out b/target/executable/transform/bpcells_regress_out/bpcells_regress_out
index 2d747dd5..50a40742 100755
--- a/target/executable/transform/bpcells_regress_out/bpcells_regress_out
+++ b/target/executable/transform/bpcells_regress_out/bpcells_regress_out
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# bpcells_regress_out v4.0.0
+# bpcells_regress_out v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -467,10 +467,10 @@ RUN pip install --user --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz"
 LABEL org.opencontainers.image.description="Companion container for running component transform bpcells_regress_out"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -587,7 +587,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bpcells_regress_out v4.0.0"
+  echo "bpcells_regress_out v4.0.1"
   echo ""
   echo "Regress out the effects of confounding variables using a linear least squares"
   echo "regression model with BPCells."
@@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "bpcells_regress_out v4.0.0"
+            echo "bpcells_regress_out v4.0.1"
             exit
             ;;
         --input)
@@ -858,7 +858,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/bpcells_regress_out:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/bpcells_regress_out:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/clr/.config.vsh.yaml b/target/executable/transform/clr/.config.vsh.yaml
index caf1bf47..a0c2d124 100644
--- a/target/executable/transform/clr/.config.vsh.yaml
+++ b/target/executable/transform/clr/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "clr"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -203,7 +203,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -240,11 +240,11 @@ build_info:
   output: "target/executable/transform/clr"
   executable: "target/executable/transform/clr/clr"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -274,7 +274,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/clr/clr b/target/executable/transform/clr/clr
index 369d1244..c507c0c0 100755
--- a/target/executable/transform/clr/clr
+++ b/target/executable/transform/clr/clr
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# clr v4.0.0
+# clr v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component transform clr"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:33Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "clr v4.0.0"
+  echo "clr v4.0.1"
   echo ""
   echo "Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017)."
   echo ""
@@ -668,7 +668,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "clr v4.0.0"
+            echo "clr v4.0.1"
             exit
             ;;
         --input)
@@ -848,7 +848,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/clr:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/clr:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/delete_layer/.config.vsh.yaml b/target/executable/transform/delete_layer/.config.vsh.yaml
index 159359b9..38715983 100644
--- a/target/executable/transform/delete_layer/.config.vsh.yaml
+++ b/target/executable/transform/delete_layer/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "delete_layer"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -186,7 +186,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -227,11 +227,11 @@ build_info:
   output: "target/executable/transform/delete_layer"
   executable: "target/executable/transform/delete_layer/delete_layer"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -261,7 +261,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/delete_layer/delete_layer b/target/executable/transform/delete_layer/delete_layer
index 2493cac1..3f163983 100755
--- a/target/executable/transform/delete_layer/delete_layer
+++ b/target/executable/transform/delete_layer/delete_layer
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# delete_layer v4.0.0
+# delete_layer v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component transform delete_layer"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:33Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "delete_layer v4.0.0"
+  echo "delete_layer v4.0.1"
   echo ""
   echo "Delete an anndata layer from one or more modalities."
   echo ""
@@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "delete_layer v4.0.0"
+            echo "delete_layer v4.0.1"
             exit
             ;;
         --input)
@@ -829,7 +829,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/delete_layer:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/delete_layer:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/log1p/.config.vsh.yaml b/target/executable/transform/log1p/.config.vsh.yaml
index c9aab988..2c539465 100644
--- a/target/executable/transform/log1p/.config.vsh.yaml
+++ b/target/executable/transform/log1p/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "log1p"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -217,7 +217,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -253,11 +253,11 @@ build_info:
   output: "target/executable/transform/log1p"
   executable: "target/executable/transform/log1p/log1p"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -287,7 +287,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/log1p/log1p b/target/executable/transform/log1p/log1p
index acb5fa52..14d238f0 100755
--- a/target/executable/transform/log1p/log1p
+++ b/target/executable/transform/log1p/log1p
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# log1p v4.0.0
+# log1p v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component transform log1p"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "log1p v4.0.0"
+  echo "log1p v4.0.1"
   echo ""
   echo "Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the"
   echo "natural logarithm unless a different base is given."
@@ -667,7 +667,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "log1p v4.0.0"
+            echo "log1p v4.0.1"
             exit
             ;;
         --input)
@@ -847,7 +847,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/log1p:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/log1p:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/move_layer/.config.vsh.yaml b/target/executable/transform/move_layer/.config.vsh.yaml
index 45bd0940..23f46d3e 100644
--- a/target/executable/transform/move_layer/.config.vsh.yaml
+++ b/target/executable/transform/move_layer/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_layer"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -176,7 +176,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -217,11 +217,11 @@ build_info:
   output: "target/executable/transform/move_layer"
   executable: "target/executable/transform/move_layer/move_layer"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -251,7 +251,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/move_layer/move_layer b/target/executable/transform/move_layer/move_layer
index f07e93d7..7a43fafd 100755
--- a/target/executable/transform/move_layer/move_layer
+++ b/target/executable/transform/move_layer/move_layer
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# move_layer v4.0.0
+# move_layer v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \
   python -c 'exec("try:\n  import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n  exit(0)\nelse:  assert int(version(\"zarr\").partition(\".\")[0]) > 2")'
 
 LABEL org.opencontainers.image.description="Companion container for running component transform move_layer"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "move_layer v4.0.0"
+  echo "move_layer v4.0.1"
   echo ""
   echo "Move a data matrix stored at the .layers or .X attributes in a MuData object to"
   echo "another layer."
@@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "move_layer v4.0.0"
+            echo "move_layer v4.0.1"
             exit
             ;;
         --input)
@@ -830,7 +830,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/move_layer:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/move_layer:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/normalize_total/.config.vsh.yaml b/target/executable/transform/normalize_total/.config.vsh.yaml
index fc4474d6..5fd4c6d3 100644
--- a/target/executable/transform/normalize_total/.config.vsh.yaml
+++ b/target/executable/transform/normalize_total/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "normalize_total"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -229,7 +229,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -271,11 +271,11 @@ build_info:
   output: "target/executable/transform/normalize_total"
   executable: "target/executable/transform/normalize_total/normalize_total"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -305,7 +305,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/normalize_total/normalize_total b/target/executable/transform/normalize_total/normalize_total
index 28ed5797..a6e7879c 100755
--- a/target/executable/transform/normalize_total/normalize_total
+++ b/target/executable/transform/normalize_total/normalize_total
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# normalize_total v4.0.0
+# normalize_total v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component transform normalize_total"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "normalize_total v4.0.0"
+  echo "normalize_total v4.0.1"
   echo ""
   echo "Normalize counts per cell."
   echo ""
@@ -683,7 +683,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "normalize_total v4.0.0"
+            echo "normalize_total v4.0.1"
             exit
             ;;
         --input)
@@ -868,7 +868,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/normalize_total:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/normalize_total:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/regress_out/.config.vsh.yaml b/target/executable/transform/regress_out/.config.vsh.yaml
index 689ca774..b19e29de 100644
--- a/target/executable/transform/regress_out/.config.vsh.yaml
+++ b/target/executable/transform/regress_out/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "regress_out"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -206,7 +206,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -248,11 +248,11 @@ build_info:
   output: "target/executable/transform/regress_out"
   executable: "target/executable/transform/regress_out/regress_out"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -282,7 +282,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/regress_out/regress_out b/target/executable/transform/regress_out/regress_out
index 38cabd04..bf4b367f 100755
--- a/target/executable/transform/regress_out/regress_out
+++ b/target/executable/transform/regress_out/regress_out
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# regress_out v4.0.0
+# regress_out v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component transform regress_out"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:32Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "regress_out v4.0.0"
+  echo "regress_out v4.0.1"
   echo ""
   echo "Regress out (mostly) unwanted sources of variation."
   echo "Uses simple linear regression. This is inspired by Seurat's regressOut function"
@@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "regress_out v4.0.0"
+            echo "regress_out v4.0.1"
             exit
             ;;
         --input)
@@ -853,7 +853,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/regress_out:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/regress_out:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/scale/.config.vsh.yaml b/target/executable/transform/scale/.config.vsh.yaml
index 81459870..e5f21701 100644
--- a/target/executable/transform/scale/.config.vsh.yaml
+++ b/target/executable/transform/scale/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scale"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -246,11 +246,11 @@ build_info:
   output: "target/executable/transform/scale"
   executable: "target/executable/transform/scale/scale"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/scale/scale b/target/executable/transform/scale/scale
index c44484a5..92bcd658 100755
--- a/target/executable/transform/scale/scale
+++ b/target/executable/transform/scale/scale
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scale v4.0.0
+# scale v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component transform scale"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:33Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scale v4.0.0"
+  echo "scale v4.0.1"
   echo ""
   echo "Scale data to unit variance and zero mean."
   echo ""
@@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scale v4.0.0"
+            echo "scale v4.0.1"
             exit
             ;;
         --input)
@@ -855,7 +855,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/scale:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/scale:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/transform/tfidf/.config.vsh.yaml b/target/executable/transform/tfidf/.config.vsh.yaml
index 1c971fd7..d21f1b50 100644
--- a/target/executable/transform/tfidf/.config.vsh.yaml
+++ b/target/executable/transform/tfidf/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tfidf"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -237,7 +237,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim-bullseye"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -277,11 +277,11 @@ build_info:
   output: "target/executable/transform/tfidf"
   executable: "target/executable/transform/tfidf/tfidf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -311,7 +311,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/transform/tfidf/tfidf b/target/executable/transform/tfidf/tfidf
index 4f1f5962..f097cdb5 100755
--- a/target/executable/transform/tfidf/tfidf
+++ b/target/executable/transform/tfidf/tfidf
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# tfidf v4.0.0
+# tfidf v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Vladimir Shitov"
 LABEL org.opencontainers.image.description="Companion container for running component transform tfidf"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:34Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "tfidf v4.0.0"
+  echo "tfidf v4.0.1"
   echo ""
   echo "Perform TF-IDF normalization of the data (typically, ATAC)."
   echo ""
@@ -691,7 +691,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "tfidf v4.0.0"
+            echo "tfidf v4.0.1"
             exit
             ;;
         --input)
@@ -904,7 +904,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/tfidf:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/tfidf:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/velocity/scvelo/.config.vsh.yaml b/target/executable/velocity/scvelo/.config.vsh.yaml
index 2c99c9d3..c5e033a3 100644
--- a/target/executable/velocity/scvelo/.config.vsh.yaml
+++ b/target/executable/velocity/scvelo/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvelo"
 namespace: "velocity"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -311,7 +311,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -356,11 +356,11 @@ build_info:
   output: "target/executable/velocity/scvelo"
   executable: "target/executable/velocity/scvelo/scvelo"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -390,7 +390,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/velocity/scvelo/scvelo b/target/executable/velocity/scvelo/scvelo
index b2b6de72..bb7172ac 100755
--- a/target/executable/velocity/scvelo/scvelo
+++ b/target/executable/velocity/scvelo/scvelo
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# scvelo v4.0.0
+# scvelo v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component velocity scvelo"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "scvelo v4.0.0"
+  echo "scvelo v4.0.1"
   echo ""
   echo "Inputs:"
   echo "    --input"
@@ -734,7 +734,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "scvelo v4.0.0"
+            echo "scvelo v4.0.1"
             exit
             ;;
         --input)
@@ -1034,7 +1034,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/scvelo:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/scvelo:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/executable/velocity/velocyto/.config.vsh.yaml b/target/executable/velocity/velocyto/.config.vsh.yaml
index 4f27cdf9..d7658edf 100644
--- a/target/executable/velocity/velocyto/.config.vsh.yaml
+++ b/target/executable/velocity/velocyto/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "velocyto"
 namespace: "velocity"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -202,7 +202,7 @@ engines:
   id: "docker"
   image: "python:3.13"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -246,11 +246,11 @@ build_info:
   output: "target/executable/velocity/velocyto"
   executable: "target/executable/velocity/velocyto/velocyto"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/executable/velocity/velocyto/velocyto b/target/executable/velocity/velocyto/velocyto
index 516b1c30..17e72693 100755
--- a/target/executable/velocity/velocyto/velocyto
+++ b/target/executable/velocity/velocyto/velocyto
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# velocyto v4.0.0
+# velocyto v4.0.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -464,10 +464,10 @@ RUN apt-get update && \
 
 LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
 LABEL org.opencontainers.image.description="Companion container for running component velocity velocyto"
-LABEL org.opencontainers.image.created="2026-01-26T10:04:30Z"
+LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z"
 LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline"
-LABEL org.opencontainers.image.revision="de02293c9e13198622b988dac952b2c8c70a1e35"
-LABEL org.opencontainers.image.version="v4.0.0"
+LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92"
+LABEL org.opencontainers.image.version="v4.0.1"
 
 VIASHDOCKER
   fi
@@ -584,7 +584,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "velocyto v4.0.0"
+  echo "velocyto v4.0.1"
   echo ""
   echo "Runs the velocity analysis on a BAM file, outputting a loom file."
   echo ""
@@ -666,7 +666,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "velocyto v4.0.0"
+            echo "velocyto v4.0.1"
             exit
             ;;
         --input)
@@ -847,7 +847,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/velocyto:v4.0.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/velocyto:v4.0.1'
   fi
 
   # print dockerfile
diff --git a/target/nextflow/annotate/celltypist/.config.vsh.yaml b/target/nextflow/annotate/celltypist/.config.vsh.yaml
index 9bb48d40..b3ff58a4 100644
--- a/target/nextflow/annotate/celltypist/.config.vsh.yaml
+++ b/target/nextflow/annotate/celltypist/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "celltypist"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -384,7 +384,7 @@ engines:
   id: "docker"
   image: "nvcr.io/nvidia/pytorch:25.11-py3"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -431,11 +431,11 @@ build_info:
   output: "target/nextflow/annotate/celltypist"
   executable: "target/nextflow/annotate/celltypist/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -465,7 +465,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/annotate/celltypist/main.nf b/target/nextflow/annotate/celltypist/main.nf
index eb4c8b9f..1f0af76d 100644
--- a/target/nextflow/annotate/celltypist/main.nf
+++ b/target/nextflow/annotate/celltypist/main.nf
@@ -1,4 +1,4 @@
-// celltypist v4.0.0
+// celltypist v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "celltypist",
   "namespace" : "annotate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3507,7 +3507,7 @@ meta = [
       "id" : "docker",
       "image" : "nvcr.io/nvidia/pytorch:25.11-py3",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3572,12 +3572,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/annotate/celltypist",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3602,7 +3602,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4200,7 +4200,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/annotate/celltypist",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/annotate/celltypist/nextflow.config b/target/nextflow/annotate/celltypist/nextflow.config
index f8ce9a9a..01e740bd 100644
--- a/target/nextflow/annotate/celltypist/nextflow.config
+++ b/target/nextflow/annotate/celltypist/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'annotate/celltypist'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm.'
   author = 'Jakub Majercik, Weiwei Schultz'
 }
diff --git a/target/nextflow/annotate/onclass/.config.vsh.yaml b/target/nextflow/annotate/onclass/.config.vsh.yaml
index decfef73..d169157e 100644
--- a/target/nextflow/annotate/onclass/.config.vsh.yaml
+++ b/target/nextflow/annotate/onclass/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "onclass"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -365,7 +365,7 @@ engines:
   id: "docker"
   image: "python:3.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -405,11 +405,11 @@ build_info:
   output: "target/nextflow/annotate/onclass"
   executable: "target/nextflow/annotate/onclass/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -439,7 +439,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/annotate/onclass/main.nf b/target/nextflow/annotate/onclass/main.nf
index 67522b4d..0d1130ac 100644
--- a/target/nextflow/annotate/onclass/main.nf
+++ b/target/nextflow/annotate/onclass/main.nf
@@ -1,4 +1,4 @@
-// onclass v4.0.0
+// onclass v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "onclass",
   "namespace" : "annotate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3478,7 +3478,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3530,12 +3530,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/annotate/onclass",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3560,7 +3560,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4211,7 +4211,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/annotate/onclass",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/annotate/onclass/nextflow.config b/target/nextflow/annotate/onclass/nextflow.config
index e8199d9e..ce108a78 100644
--- a/target/nextflow/annotate/onclass/nextflow.config
+++ b/target/nextflow/annotate/onclass/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'annotate/onclass'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'OnClass is a python package for single-cell cell type annotation. It uses the Cell Ontology to capture the cell type similarity. \nThese similarities enable OnClass to annotate cell types that are never seen in the training data.\n'
   author = 'Jakub Majercik'
 }
diff --git a/target/nextflow/annotate/popv/.config.vsh.yaml b/target/nextflow/annotate/popv/.config.vsh.yaml
index badb67c5..b78451d3 100644
--- a/target/nextflow/annotate/popv/.config.vsh.yaml
+++ b/target/nextflow/annotate/popv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "popv"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Matthias Beyens"
   roles:
@@ -310,7 +310,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -361,11 +361,11 @@ build_info:
   output: "target/nextflow/annotate/popv"
   executable: "target/nextflow/annotate/popv/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -395,7 +395,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/annotate/popv/main.nf b/target/nextflow/annotate/popv/main.nf
index b9f5ebb8..55cf6801 100644
--- a/target/nextflow/annotate/popv/main.nf
+++ b/target/nextflow/annotate/popv/main.nf
@@ -1,4 +1,4 @@
-// popv v4.0.0
+// popv v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "popv",
   "namespace" : "annotate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Matthias Beyens",
@@ -3421,7 +3421,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3492,12 +3492,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/annotate/popv",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3522,7 +3522,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4172,7 +4172,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/annotate/popv",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/annotate/popv/nextflow.config b/target/nextflow/annotate/popv/nextflow.config
index 31e58b63..5ea1d455 100644
--- a/target/nextflow/annotate/popv/nextflow.config
+++ b/target/nextflow/annotate/popv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'annotate/popv'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs popular major vote cell typing on single cell sequence data using multiple algorithms. Note that this is a one-shot version of PopV.'
   author = 'Matthias Beyens, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml b/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml
index 4ff6f822..01c22e05 100644
--- a/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml
+++ b/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "random_forest_annotation"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -373,7 +373,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -420,11 +420,11 @@ build_info:
   output: "target/nextflow/annotate/random_forest_annotation"
   executable: "target/nextflow/annotate/random_forest_annotation/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -454,7 +454,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/annotate/random_forest_annotation/main.nf b/target/nextflow/annotate/random_forest_annotation/main.nf
index 5a8ee0ab..e1f01208 100644
--- a/target/nextflow/annotate/random_forest_annotation/main.nf
+++ b/target/nextflow/annotate/random_forest_annotation/main.nf
@@ -1,4 +1,4 @@
-// random_forest_annotation v4.0.0
+// random_forest_annotation v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "random_forest_annotation",
   "namespace" : "annotate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3481,7 +3481,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3546,12 +3546,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/annotate/random_forest_annotation",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3576,7 +3576,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4171,7 +4171,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/annotate/random_forest_annotation",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/annotate/random_forest_annotation/nextflow.config b/target/nextflow/annotate/random_forest_annotation/nextflow.config
index a80589b8..3d784e80 100644
--- a/target/nextflow/annotate/random_forest_annotation/nextflow.config
+++ b/target/nextflow/annotate/random_forest_annotation/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'annotate/random_forest_annotation'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Automated cell type annotation tool for scRNA-seq datasets on the basis of random forest.'
   author = 'Jakub Majercik'
 }
diff --git a/target/nextflow/annotate/scanvi/.config.vsh.yaml b/target/nextflow/annotate/scanvi/.config.vsh.yaml
index 59c0d4cb..dbc085ac 100644
--- a/target/nextflow/annotate/scanvi/.config.vsh.yaml
+++ b/target/nextflow/annotate/scanvi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanvi"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -405,7 +405,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -442,11 +442,11 @@ build_info:
   output: "target/nextflow/annotate/scanvi"
   executable: "target/nextflow/annotate/scanvi/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -476,7 +476,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/annotate/scanvi/main.nf b/target/nextflow/annotate/scanvi/main.nf
index b13b7494..624d204b 100644
--- a/target/nextflow/annotate/scanvi/main.nf
+++ b/target/nextflow/annotate/scanvi/main.nf
@@ -1,4 +1,4 @@
-// scanvi v4.0.0
+// scanvi v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scanvi",
   "namespace" : "annotate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3542,7 +3542,7 @@ meta = [
       "id" : "docker",
       "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3590,12 +3590,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/annotate/scanvi",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3620,7 +3620,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4170,7 +4170,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/annotate/scanvi",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midcpu",
diff --git a/target/nextflow/annotate/scanvi/nextflow.config b/target/nextflow/annotate/scanvi/nextflow.config
index 3ef20f78..25ca04dd 100644
--- a/target/nextflow/annotate/scanvi/nextflow.config
+++ b/target/nextflow/annotate/scanvi/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'annotate/scanvi'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'scANVI () is a semi-supervised model for single-cell transcriptomics data. scANVI is an scVI extension that can leverage the cell type knowledge for a subset of the cells present in the data sets to infer the states of the rest of the cells.\nThis component will instantiate a scANVI model from a pre-trained scVI model, integrate the data and perform label prediction.\n'
   author = 'Dorien Roosen, Jakub Majercik, Weiwei Schultz'
 }
diff --git a/target/nextflow/annotate/singler/.config.vsh.yaml b/target/nextflow/annotate/singler/.config.vsh.yaml
index 707e6ec1..171380f3 100644
--- a/target/nextflow/annotate/singler/.config.vsh.yaml
+++ b/target/nextflow/annotate/singler/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "singler"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -424,7 +424,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -483,11 +483,11 @@ build_info:
   output: "target/nextflow/annotate/singler"
   executable: "target/nextflow/annotate/singler/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -517,7 +517,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/annotate/singler/main.nf b/target/nextflow/annotate/singler/main.nf
index 4f08ab67..29e90424 100644
--- a/target/nextflow/annotate/singler/main.nf
+++ b/target/nextflow/annotate/singler/main.nf
@@ -1,4 +1,4 @@
-// singler v4.0.0
+// singler v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "singler",
   "namespace" : "annotate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3524,7 +3524,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3605,12 +3605,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/annotate/singler",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3635,7 +3635,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4277,7 +4277,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/annotate/singler",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/annotate/singler/nextflow.config b/target/nextflow/annotate/singler/nextflow.config
index 6d13e9a2..215c4f92 100644
--- a/target/nextflow/annotate/singler/nextflow.config
+++ b/target/nextflow/annotate/singler/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'annotate/singler'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'SingleR performs reference-based cell type annotation for single-cell RNA-seq data \nby computing Spearman correlations between test cells and reference samples with known labels, \nusing marker genes to assign the most similar cell type label to each new cell.\n'
   author = 'Dorien Roosen, Weiwei Schultz'
 }
diff --git a/target/nextflow/annotate/svm_annotation/.config.vsh.yaml b/target/nextflow/annotate/svm_annotation/.config.vsh.yaml
index 525fbbc4..536c9721 100644
--- a/target/nextflow/annotate/svm_annotation/.config.vsh.yaml
+++ b/target/nextflow/annotate/svm_annotation/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "svm_annotation"
 namespace: "annotate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -356,7 +356,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -403,11 +403,11 @@ build_info:
   output: "target/nextflow/annotate/svm_annotation"
   executable: "target/nextflow/annotate/svm_annotation/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -437,7 +437,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/annotate/svm_annotation/main.nf b/target/nextflow/annotate/svm_annotation/main.nf
index b3e50bc1..c446935a 100644
--- a/target/nextflow/annotate/svm_annotation/main.nf
+++ b/target/nextflow/annotate/svm_annotation/main.nf
@@ -1,4 +1,4 @@
-// svm_annotation v4.0.0
+// svm_annotation v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "svm_annotation",
   "namespace" : "annotate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3468,7 +3468,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3533,12 +3533,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/annotate/svm_annotation",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3563,7 +3563,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4141,7 +4141,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/annotate/svm_annotation",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/annotate/svm_annotation/nextflow.config b/target/nextflow/annotate/svm_annotation/nextflow.config
index fdac3154..f4ff1f6f 100644
--- a/target/nextflow/annotate/svm_annotation/nextflow.config
+++ b/target/nextflow/annotate/svm_annotation/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'annotate/svm_annotation'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Automated cell type annotation tool for scRNA-seq datasets on the basis of SVMs.'
   author = 'Jakub Majercik'
 }
diff --git a/target/nextflow/cluster/leiden/.config.vsh.yaml b/target/nextflow/cluster/leiden/.config.vsh.yaml
index 8a4ec974..68a1032d 100644
--- a/target/nextflow/cluster/leiden/.config.vsh.yaml
+++ b/target/nextflow/cluster/leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "leiden"
 namespace: "cluster"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -215,7 +215,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -258,11 +258,11 @@ build_info:
   output: "target/nextflow/cluster/leiden"
   executable: "target/nextflow/cluster/leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/cluster/leiden/main.nf b/target/nextflow/cluster/leiden/main.nf
index c2599931..ba1c8c67 100644
--- a/target/nextflow/cluster/leiden/main.nf
+++ b/target/nextflow/cluster/leiden/main.nf
@@ -1,4 +1,4 @@
-// leiden v4.0.0
+// leiden v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "leiden",
   "namespace" : "cluster",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3294,7 +3294,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3352,12 +3352,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cluster/leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3382,7 +3382,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4147,7 +4147,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/cluster/leiden",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/cluster/leiden/nextflow.config b/target/nextflow/cluster/leiden/nextflow.config
index f8d69f99..83a52fd5 100644
--- a/target/nextflow/cluster/leiden/nextflow.config
+++ b/target/nextflow/cluster/leiden/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'cluster/leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18]. \nLeiden is an improved version of the [Louvain algorithm] [Blondel08]. \nIt has been proposed for single-cell analysis by [Levine15] [Levine15]. \nThis requires having ran `neighbors/find_neighbors` or `neighbors/bbknn` first.\n\n[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in large networks, J. Stat. Mech.  \n[Levine15]: Levine et al. (2015), Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis, Cell.  \n[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing well-connected communities arXiv.  \n[Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology.  \n'
   author = 'Dries De Maeyer'
 }
diff --git a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml
index 511739cc..1cd1ae52 100644
--- a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml
+++ b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "compress_h5mu"
 namespace: "compression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -157,7 +157,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -198,11 +198,11 @@ build_info:
   output: "target/nextflow/compression/compress_h5mu"
   executable: "target/nextflow/compression/compress_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -232,7 +232,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/compression/compress_h5mu/main.nf b/target/nextflow/compression/compress_h5mu/main.nf
index 5e285aec..b3d7dbc4 100644
--- a/target/nextflow/compression/compress_h5mu/main.nf
+++ b/target/nextflow/compression/compress_h5mu/main.nf
@@ -1,4 +1,4 @@
-// compress_h5mu v4.0.0
+// compress_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "compress_h5mu",
   "namespace" : "compression",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3236,7 +3236,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3292,12 +3292,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/compression/compress_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3322,7 +3322,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3772,7 +3772,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/compression/compress_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/compression/compress_h5mu/nextflow.config b/target/nextflow/compression/compress_h5mu/nextflow.config
index 92c548dc..4ccc42ed 100644
--- a/target/nextflow/compression/compress_h5mu/nextflow.config
+++ b/target/nextflow/compression/compress_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'compression/compress_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Compress a MuData file. \n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/compression/tar_extract/.config.vsh.yaml b/target/nextflow/compression/tar_extract/.config.vsh.yaml
index c5906558..f6155a66 100644
--- a/target/nextflow/compression/tar_extract/.config.vsh.yaml
+++ b/target/nextflow/compression/tar_extract/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tar_extract"
 namespace: "compression"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -157,7 +157,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -170,11 +170,11 @@ build_info:
   output: "target/nextflow/compression/tar_extract"
   executable: "target/nextflow/compression/tar_extract/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -204,7 +204,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/compression/tar_extract/main.nf b/target/nextflow/compression/tar_extract/main.nf
index 03dca75a..32b7356f 100644
--- a/target/nextflow/compression/tar_extract/main.nf
+++ b/target/nextflow/compression/tar_extract/main.nf
@@ -1,4 +1,4 @@
-// tar_extract v4.0.0
+// tar_extract v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "tar_extract",
   "namespace" : "compression",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3225,7 +3225,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/"
     },
     {
@@ -3239,12 +3239,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/compression/tar_extract",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3269,7 +3269,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3722,7 +3722,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/compression/tar_extract",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/compression/tar_extract/nextflow.config b/target/nextflow/compression/tar_extract/nextflow.config
index de6e54de..8c7da9f7 100644
--- a/target/nextflow/compression/tar_extract/nextflow.config
+++ b/target/nextflow/compression/tar_extract/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'compression/tar_extract'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Extract files from a tar archive'
 }
 
diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml
index 76a4254b..068def9c 100644
--- a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_10xh5_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -263,7 +263,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -305,11 +305,11 @@ build_info:
   output: "target/nextflow/convert/from_10xh5_to_h5mu"
   executable: "target/nextflow/convert/from_10xh5_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -339,7 +339,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf
index 48c073d3..b555eee0 100644
--- a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// from_10xh5_to_h5mu v4.0.0
+// from_10xh5_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_10xh5_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3394,7 +3394,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3451,12 +3451,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_10xh5_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3481,7 +3481,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3988,7 +3988,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_10xh5_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config b/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config
index 650b692a..c545bcaf 100644
--- a/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_10xh5_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts a 10x h5 into an h5mu file.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml
index ab1ab5d5..d9e96736 100644
--- a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_10xmtx_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -164,7 +164,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -206,11 +206,11 @@ build_info:
   output: "target/nextflow/convert/from_10xmtx_to_h5mu"
   executable: "target/nextflow/convert/from_10xmtx_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -240,7 +240,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf
index 880d4adb..f8708724 100644
--- a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// from_10xmtx_to_h5mu v4.0.0
+// from_10xmtx_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_10xmtx_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3247,7 +3247,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3304,12 +3304,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_10xmtx_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3334,7 +3334,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3802,7 +3802,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_10xmtx_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config b/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config
index 491860cd..7d4962ed 100644
--- a/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_10xmtx_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts a 10x mtx into an h5mu file.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml
index e75ae3d8..85448fd2 100644
--- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml
+++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_bd_to_10x_molecular_barcode_tags"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -161,7 +161,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -179,11 +179,11 @@ build_info:
   output: "target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags"
   executable: "target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -213,7 +213,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf
index 577d39ef..81c0435c 100644
--- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf
+++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf
@@ -1,4 +1,4 @@
-// from_bd_to_10x_molecular_barcode_tags v4.0.0
+// from_bd_to_10x_molecular_barcode_tags v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_bd_to_10x_molecular_barcode_tags",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3240,7 +3240,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3263,12 +3263,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3293,7 +3293,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3800,7 +3800,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_bd_to_10x_molecular_barcode_tags",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config
index c59f1f6b..58f4ac95 100644
--- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config
+++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_bd_to_10x_molecular_barcode_tags'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB).\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml
index 0ac6738d..a8d39b54 100644
--- a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_bdrhap_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -190,7 +190,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -219,11 +219,11 @@ build_info:
   output: "target/nextflow/convert/from_bdrhap_to_h5mu"
   executable: "target/nextflow/convert/from_bdrhap_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -253,7 +253,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf
index 265baec3..d30a8ec3 100644
--- a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// from_bdrhap_to_h5mu v4.0.0
+// from_bdrhap_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_bdrhap_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3288,7 +3288,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3324,12 +3324,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_bdrhap_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3354,7 +3354,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3839,7 +3839,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_bdrhap_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config b/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config
index bc82b770..05e7ac70 100644
--- a/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_bdrhap_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file.\n'
   author = 'Dorien Roosen, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml
index ea0b092b..5f67ddb3 100644
--- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_cellranger_multi_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -208,7 +208,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -245,11 +245,11 @@ build_info:
   output: "target/nextflow/convert/from_cellranger_multi_to_h5mu"
   executable: "target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -279,7 +279,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf
index 449258b5..a002de9c 100644
--- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// from_cellranger_multi_to_h5mu v4.0.0
+// from_cellranger_multi_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_cellranger_multi_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3304,7 +3304,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3352,12 +3352,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_cellranger_multi_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3382,7 +3382,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4279,7 +4279,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_cellranger_multi_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config b/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config
index 989ed06f..bbca3c37 100644
--- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_cellranger_multi_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts the output from cellranger multi to a single .h5mu file.\nBy default, will map the following library type names to modality names:\n  - Gene Expression: rna\n  - Peaks: atac\n  - Antibody Capture: prot\n  - VDJ: vdj\n  - VDJ-T: vdj_t\n  - VDJ-B: vdj_b\n  - CRISPR Guide Capture: crispr\n  - Multiplexing Capture: hashing\n  \nOther library types have their whitepace removed and dashes replaced by\nunderscores to generate the modality name.\n\nCurrently does not allow parsing the output from cell barcode demultiplexing.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml
index e8b801aa..709f0e6c 100644
--- a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5ad_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -173,7 +173,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -214,11 +214,11 @@ build_info:
   output: "target/nextflow/convert/from_h5ad_to_h5mu"
   executable: "target/nextflow/convert/from_h5ad_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf
index e82e874b..4d3c86b6 100644
--- a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// from_h5ad_to_h5mu v4.0.0
+// from_h5ad_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_h5ad_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3253,7 +3253,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3309,12 +3309,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5ad_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3339,7 +3339,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3813,7 +3813,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_h5ad_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config b/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config
index 3fc0ed64..ed4269ac 100644
--- a/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_h5ad_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts a single layer h5ad file into a single MuData object\n'
   author = 'Dries De Maeyer'
 }
diff --git a/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml b/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml
index de5999e9..a6ff443f 100644
--- a/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5ad_to_seurat"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -196,11 +196,11 @@ build_info:
   output: "target/nextflow/convert/from_h5ad_to_seurat"
   executable: "target/nextflow/convert/from_h5ad_to_seurat/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -230,7 +230,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_h5ad_to_seurat/main.nf b/target/nextflow/convert/from_h5ad_to_seurat/main.nf
index dbda22db..8a3ce97f 100644
--- a/target/nextflow/convert/from_h5ad_to_seurat/main.nf
+++ b/target/nextflow/convert/from_h5ad_to_seurat/main.nf
@@ -1,4 +1,4 @@
-// from_h5ad_to_seurat v4.0.0
+// from_h5ad_to_seurat v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_h5ad_to_seurat",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3240,7 +3240,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3291,12 +3291,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5ad_to_seurat",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3321,7 +3321,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3783,7 +3783,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_h5ad_to_seurat",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config b/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config
index a87bcc7e..ac9285dc 100644
--- a/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config
+++ b/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_h5ad_to_seurat'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts an h5ad file into a Seurat file.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml
index 58427d67..0abdc94b 100644
--- a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_or_h5ad_to_seurat"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -166,7 +166,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -205,11 +205,11 @@ build_info:
   output: "target/nextflow/convert/from_h5mu_or_h5ad_to_seurat"
   executable: "target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -239,7 +239,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf
index 520665d5..b7700999 100644
--- a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf
+++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf
@@ -1,4 +1,4 @@
-// from_h5mu_or_h5ad_to_seurat v4.0.0
+// from_h5mu_or_h5ad_to_seurat v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_h5mu_or_h5ad_to_seurat",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3246,7 +3246,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3299,12 +3299,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3329,7 +3329,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3853,7 +3853,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_h5mu_or_h5ad_to_seurat",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config
index aac6b0e4..3530c19a 100644
--- a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config
+++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_h5mu_or_h5ad_to_seurat'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts an h5ad file or a single modality of an h5mu file into a Seurat file.\n'
   author = 'Dorien Roosen'
 }
diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml
index 9b0698e0..66cb9815 100644
--- a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_or_h5ad_to_tiledb"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -334,7 +334,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -381,11 +381,11 @@ build_info:
   output: "target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb"
   executable: "target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -415,7 +415,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf
index 3e51fce2..b688d1de 100644
--- a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf
+++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf
@@ -1,4 +1,4 @@
-// from_h5mu_or_h5ad_to_tiledb v4.0.0
+// from_h5mu_or_h5ad_to_tiledb v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_h5mu_or_h5ad_to_tiledb",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3438,7 +3438,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3503,12 +3503,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3533,7 +3533,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4666,7 +4666,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_h5mu_or_h5ad_to_tiledb",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config
index 12bb77bd..0e78c654 100644
--- a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config
+++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_h5mu_or_h5ad_to_tiledb'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert a MuData or AnnData object to tiledb. Currently, transcriptome and protein modalities are supported.\n\nNOTE: The functionality provided by this component is experimental and may be subject to change. \n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml
index c93573bc..ccf37ce1 100644
--- a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_to_h5ad"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -174,7 +174,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -215,11 +215,11 @@ build_info:
   output: "target/nextflow/convert/from_h5mu_to_h5ad"
   executable: "target/nextflow/convert/from_h5mu_to_h5ad/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -249,7 +249,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf
index 7c44c7e6..79b88792 100644
--- a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf
+++ b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf
@@ -1,4 +1,4 @@
-// from_h5mu_to_h5ad v4.0.0
+// from_h5mu_to_h5ad v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_h5mu_to_h5ad",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3259,7 +3259,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3315,12 +3315,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_h5ad",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3345,7 +3345,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3806,7 +3806,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_h5mu_to_h5ad",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config b/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config
index 8a4a2ec4..8c37f0c3 100644
--- a/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config
+++ b/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_h5mu_to_h5ad'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts a h5mu file into a h5ad file.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml
index 09ff6c51..ca586cea 100644
--- a/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml
+++ b/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_h5mu_to_seurat"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -155,7 +155,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -188,11 +188,11 @@ build_info:
   output: "target/nextflow/convert/from_h5mu_to_seurat"
   executable: "target/nextflow/convert/from_h5mu_to_seurat/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -222,7 +222,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_h5mu_to_seurat/main.nf b/target/nextflow/convert/from_h5mu_to_seurat/main.nf
index 35dc4ae0..e35036c3 100644
--- a/target/nextflow/convert/from_h5mu_to_seurat/main.nf
+++ b/target/nextflow/convert/from_h5mu_to_seurat/main.nf
@@ -1,4 +1,4 @@
-// from_h5mu_to_seurat v4.0.0
+// from_h5mu_to_seurat v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_h5mu_to_seurat",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3228,7 +3228,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3271,12 +3271,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_seurat",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3301,7 +3301,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3821,7 +3821,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_h5mu_to_seurat",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config b/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config
index e2b88db5..211241c5 100644
--- a/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config
+++ b/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_h5mu_to_seurat'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts an h5mu file into a Seurat file.\n\nRestrictions:\n  - Only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation.\n  - Multimodal embeddings (global .obsm slot) are loaded with the assay.used field set to the default assay.\n  - Embeddings names are changed in order to comply with R & Seurat requirements and conventions.\n  - Feature names with underscores (\'_\') are automatically replaced with dashes (\'-\')\n  - Seurat does not support global variables metadata /var.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml
index a8be8c46..92659130 100644
--- a/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_seurat_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -312,7 +312,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -388,11 +388,11 @@ build_info:
   output: "target/nextflow/convert/from_seurat_to_h5mu"
   executable: "target/nextflow/convert/from_seurat_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -422,7 +422,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_seurat_to_h5mu/main.nf b/target/nextflow/convert/from_seurat_to_h5mu/main.nf
index 1dbb2663..13ccc978 100644
--- a/target/nextflow/convert/from_seurat_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_seurat_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// from_seurat_to_h5mu v4.0.0
+// from_seurat_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_seurat_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3401,7 +3401,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3505,12 +3505,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_seurat_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3535,7 +3535,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4062,7 +4062,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_seurat_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config b/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config
index 70e89818..eb40fee6 100644
--- a/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_seurat_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Converts a Seurat file into an H5MU file.\n'
   author = 'Dorien Roosen'
 }
diff --git a/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml
index 1fa5e886..a5daacad 100644
--- a/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "from_tiledb_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -214,7 +214,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -258,11 +258,11 @@ build_info:
   output: "target/nextflow/convert/from_tiledb_to_h5mu"
   executable: "target/nextflow/convert/from_tiledb_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/from_tiledb_to_h5mu/main.nf b/target/nextflow/convert/from_tiledb_to_h5mu/main.nf
index a96ce896..a490c6b0 100644
--- a/target/nextflow/convert/from_tiledb_to_h5mu/main.nf
+++ b/target/nextflow/convert/from_tiledb_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// from_tiledb_to_h5mu v4.0.0
+// from_tiledb_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "from_tiledb_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3303,7 +3303,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3362,12 +3362,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/from_tiledb_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3392,7 +3392,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3935,7 +3935,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/from_tiledb_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config b/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config
index 60a4cc26..720dac4b 100644
--- a/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/from_tiledb_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   author = 'Dries Schaumont'
 }
 
diff --git a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml
index 0cf56c10..b37be983 100644
--- a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "velocyto_to_h5mu"
 namespace: "convert"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -244,7 +244,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -275,11 +275,11 @@ build_info:
   output: "target/nextflow/convert/velocyto_to_h5mu"
   executable: "target/nextflow/convert/velocyto_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -309,7 +309,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/convert/velocyto_to_h5mu/main.nf b/target/nextflow/convert/velocyto_to_h5mu/main.nf
index 9b65676b..04f0b6a5 100644
--- a/target/nextflow/convert/velocyto_to_h5mu/main.nf
+++ b/target/nextflow/convert/velocyto_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// velocyto_to_h5mu v4.0.0
+// velocyto_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "velocyto_to_h5mu",
   "namespace" : "convert",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3355,7 +3355,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3393,12 +3393,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/convert/velocyto_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3423,7 +3423,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3913,7 +3913,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/convert/velocyto_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/convert/velocyto_to_h5mu/nextflow.config b/target/nextflow/convert/velocyto_to_h5mu/nextflow.config
index c2b9dcaa..7a2c7f4f 100644
--- a/target/nextflow/convert/velocyto_to_h5mu/nextflow.config
+++ b/target/nextflow/convert/velocyto_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'convert/velocyto_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert a velocyto loom file to a h5mu file.\n\nIf an input h5mu file is also provided, the velocity\nh5ad object will get added to that h5mu instead.\n'
   author = 'Dries Schaumont, Robrecht Cannoodt, Angela Oliveira Pisco'
 }
diff --git a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml
index 563b0167..279ac1c7 100644
--- a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml
+++ b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellbender_remove_background"
 namespace: "correction"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Inputs"
   arguments:
@@ -578,7 +578,7 @@ engines:
   id: "docker"
   image: "nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -611,11 +611,11 @@ build_info:
   output: "target/nextflow/correction/cellbender_remove_background"
   executable: "target/nextflow/correction/cellbender_remove_background/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -645,7 +645,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/correction/cellbender_remove_background/main.nf b/target/nextflow/correction/cellbender_remove_background/main.nf
index 18a5f2ce..0bb0d4b4 100644
--- a/target/nextflow/correction/cellbender_remove_background/main.nf
+++ b/target/nextflow/correction/cellbender_remove_background/main.nf
@@ -1,4 +1,4 @@
-// cellbender_remove_background v4.0.0
+// cellbender_remove_background v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellbender_remove_background",
   "namespace" : "correction",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "argument_groups" : [
     {
       "name" : "Inputs",
@@ -3659,7 +3659,7 @@ meta = [
       "id" : "docker",
       "image" : "nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3696,12 +3696,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/correction/cellbender_remove_background",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3726,7 +3726,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4404,7 +4404,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/correction/cellbender_remove_background",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midcpu",
diff --git a/target/nextflow/correction/cellbender_remove_background/nextflow.config b/target/nextflow/correction/cellbender_remove_background/nextflow.config
index 13622124..6300b267 100644
--- a/target/nextflow/correction/cellbender_remove_background/nextflow.config
+++ b/target/nextflow/correction/cellbender_remove_background/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'correction/cellbender_remove_background'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.\n\nThis module removes counts due to ambient RNA molecules and random barcode swapping from (raw) UMI-based scRNA-seq count matrices. \nAt the moment, only the count matrices produced by the CellRanger count pipeline is supported. Support for additional tools and protocols \nwill be added in the future. A quick start tutorial can be found here.\n\nFleming et al. 2022, bioRxiv.\n'
 }
 
diff --git a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml
index 479329b1..99df40db 100644
--- a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml
+++ b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "concatenate_h5mu"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -253,7 +253,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -300,11 +300,11 @@ build_info:
   output: "target/nextflow/dataflow/concatenate_h5mu"
   executable: "target/nextflow/dataflow/concatenate_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -334,7 +334,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dataflow/concatenate_h5mu/main.nf b/target/nextflow/dataflow/concatenate_h5mu/main.nf
index cfd315ad..f32e613f 100644
--- a/target/nextflow/dataflow/concatenate_h5mu/main.nf
+++ b/target/nextflow/dataflow/concatenate_h5mu/main.nf
@@ -1,4 +1,4 @@
-// concatenate_h5mu v4.0.0
+// concatenate_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "concatenate_h5mu",
   "namespace" : "dataflow",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3328,7 +3328,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3393,12 +3393,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/concatenate_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3423,7 +3423,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4266,7 +4266,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/concatenate_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midcpu",
diff --git a/target/nextflow/dataflow/concatenate_h5mu/nextflow.config b/target/nextflow/dataflow/concatenate_h5mu/nextflow.config
index 47f4ccf3..b8b3566b 100644
--- a/target/nextflow/dataflow/concatenate_h5mu/nextflow.config
+++ b/target/nextflow/dataflow/concatenate_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/concatenate_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Concatenate observations from samples in several (uni- and/or multi-modal) MuData files into a single file.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/dataflow/merge/.config.vsh.yaml b/target/nextflow/dataflow/merge/.config.vsh.yaml
index a29e9741..200bb1ba 100644
--- a/target/nextflow/dataflow/merge/.config.vsh.yaml
+++ b/target/nextflow/dataflow/merge/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "merge"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -163,7 +163,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -204,11 +204,11 @@ build_info:
   output: "target/nextflow/dataflow/merge"
   executable: "target/nextflow/dataflow/merge/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -238,7 +238,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dataflow/merge/main.nf b/target/nextflow/dataflow/merge/main.nf
index ea556608..98655694 100644
--- a/target/nextflow/dataflow/merge/main.nf
+++ b/target/nextflow/dataflow/merge/main.nf
@@ -1,4 +1,4 @@
-// merge v4.0.0
+// merge v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "merge",
   "namespace" : "dataflow",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3246,7 +3246,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3302,12 +3302,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/merge",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3332,7 +3332,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3847,7 +3847,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/merge",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/dataflow/merge/nextflow.config b/target/nextflow/dataflow/merge/nextflow.config
index 777ee540..c57d0781 100644
--- a/target/nextflow/dataflow/merge/nextflow.config
+++ b/target/nextflow/dataflow/merge/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/merge'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Combine one or more single-modality .h5mu files together into one .h5mu file.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml b/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml
index a08d5fca..55e6f3fe 100644
--- a/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml
+++ b/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_h5mu"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -203,7 +203,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -244,11 +244,11 @@ build_info:
   output: "target/nextflow/dataflow/split_h5mu"
   executable: "target/nextflow/dataflow/split_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -278,7 +278,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dataflow/split_h5mu/main.nf b/target/nextflow/dataflow/split_h5mu/main.nf
index 543ebc4e..c31ca576 100644
--- a/target/nextflow/dataflow/split_h5mu/main.nf
+++ b/target/nextflow/dataflow/split_h5mu/main.nf
@@ -1,4 +1,4 @@
-// split_h5mu v4.0.0
+// split_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_h5mu",
   "namespace" : "dataflow",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3285,7 +3285,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3341,12 +3341,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/split_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3371,7 +3371,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3908,7 +3908,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/split_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/dataflow/split_h5mu/nextflow.config b/target/nextflow/dataflow/split_h5mu/nextflow.config
index 72e0c970..d60d18b8 100644
--- a/target/nextflow/dataflow/split_h5mu/nextflow.config
+++ b/target/nextflow/dataflow/split_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/split_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. \n'
   author = 'Dorien Roosen'
 }
diff --git a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml
index e98b2747..55701c3f 100644
--- a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml
+++ b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "split_modalities"
 namespace: "dataflow"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -190,7 +190,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -231,11 +231,11 @@ build_info:
   output: "target/nextflow/dataflow/split_modalities"
   executable: "target/nextflow/dataflow/split_modalities/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -265,7 +265,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dataflow/split_modalities/main.nf b/target/nextflow/dataflow/split_modalities/main.nf
index cbd9f52a..ebda9586 100644
--- a/target/nextflow/dataflow/split_modalities/main.nf
+++ b/target/nextflow/dataflow/split_modalities/main.nf
@@ -1,4 +1,4 @@
-// split_modalities v4.0.0
+// split_modalities v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "split_modalities",
   "namespace" : "dataflow",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3280,7 +3280,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3336,12 +3336,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dataflow/split_modalities",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3366,7 +3366,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3865,7 +3865,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dataflow/split_modalities",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/dataflow/split_modalities/nextflow.config b/target/nextflow/dataflow/split_modalities/nextflow.config
index 15a4d6b3..11770fe7 100644
--- a/target/nextflow/dataflow/split_modalities/nextflow.config
+++ b/target/nextflow/dataflow/split_modalities/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dataflow/split_modalities'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files. \n'
   author = 'Dries Schaumont, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml
index f196b82d..b38b3f75 100644
--- a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml
+++ b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bcl2fastq"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Toni Verbeiren"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/bcl2fastq:2.20"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -196,11 +196,11 @@ build_info:
   output: "target/nextflow/demux/bcl2fastq"
   executable: "target/nextflow/demux/bcl2fastq/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -230,7 +230,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/demux/bcl2fastq/main.nf b/target/nextflow/demux/bcl2fastq/main.nf
index 479b18e8..8c2578de 100644
--- a/target/nextflow/demux/bcl2fastq/main.nf
+++ b/target/nextflow/demux/bcl2fastq/main.nf
@@ -1,4 +1,4 @@
-// bcl2fastq v4.0.0
+// bcl2fastq v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bcl2fastq",
   "namespace" : "demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Toni Verbeiren",
@@ -3259,7 +3259,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/bcl2fastq:2.20",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3282,12 +3282,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/demux/bcl2fastq",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3312,7 +3312,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3771,7 +3771,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/demux/bcl2fastq",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/demux/bcl2fastq/nextflow.config b/target/nextflow/demux/bcl2fastq/nextflow.config
index 5e2731c8..ec6b8843 100644
--- a/target/nextflow/demux/bcl2fastq/nextflow.config
+++ b/target/nextflow/demux/bcl2fastq/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'demux/bcl2fastq'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert bcl files to fastq files using bcl2fastq.\n'
   author = 'Toni Verbeiren'
 }
diff --git a/target/nextflow/demux/bcl_convert/.config.vsh.yaml b/target/nextflow/demux/bcl_convert/.config.vsh.yaml
index 4bd1739b..15830b17 100644
--- a/target/nextflow/demux/bcl_convert/.config.vsh.yaml
+++ b/target/nextflow/demux/bcl_convert/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bcl_convert"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Toni Verbeiren"
   roles:
@@ -250,7 +250,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/bclconvert:4.2"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -268,11 +268,11 @@ build_info:
   output: "target/nextflow/demux/bcl_convert"
   executable: "target/nextflow/demux/bcl_convert/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -302,7 +302,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/demux/bcl_convert/main.nf b/target/nextflow/demux/bcl_convert/main.nf
index ecea87c9..97eac16a 100644
--- a/target/nextflow/demux/bcl_convert/main.nf
+++ b/target/nextflow/demux/bcl_convert/main.nf
@@ -1,4 +1,4 @@
-// bcl_convert v4.0.0
+// bcl_convert v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3038,7 +3038,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bcl_convert",
   "namespace" : "demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Toni Verbeiren",
@@ -3363,7 +3363,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/bclconvert:4.2",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3386,12 +3386,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/demux/bcl_convert",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3416,7 +3416,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3882,7 +3882,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/demux/bcl_convert",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/demux/bcl_convert/nextflow.config b/target/nextflow/demux/bcl_convert/nextflow.config
index bcbec47a..ec032a1f 100644
--- a/target/nextflow/demux/bcl_convert/nextflow.config
+++ b/target/nextflow/demux/bcl_convert/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'demux/bcl_convert'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\nhttps://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html\nand https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html\n'
   author = 'Toni Verbeiren, Marijke Van Moerbeke, Weiwei Schultz, Dorien Roosen'
 }
diff --git a/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml b/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml
index c29d3b8f..cd87966f 100644
--- a/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml
+++ b/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_atac_mkfastq"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -213,7 +213,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger_atac:2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -237,11 +237,11 @@ build_info:
   output: "target/nextflow/demux/cellranger_atac_mkfastq"
   executable: "target/nextflow/demux/cellranger_atac_mkfastq/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -271,7 +271,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/demux/cellranger_atac_mkfastq/main.nf b/target/nextflow/demux/cellranger_atac_mkfastq/main.nf
index 9403bb35..7855c9ba 100644
--- a/target/nextflow/demux/cellranger_atac_mkfastq/main.nf
+++ b/target/nextflow/demux/cellranger_atac_mkfastq/main.nf
@@ -1,4 +1,4 @@
-// cellranger_atac_mkfastq v4.0.0
+// cellranger_atac_mkfastq v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_atac_mkfastq",
   "namespace" : "demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3295,7 +3295,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/cellranger_atac:2.1",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3327,12 +3327,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/demux/cellranger_atac_mkfastq",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3357,7 +3357,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3852,7 +3852,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/demux/cellranger_atac_mkfastq",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config b/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config
index 770ae87e..bb6fca46 100644
--- a/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config
+++ b/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'demux/cellranger_atac_mkfastq'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Demultiplex raw sequencing data for ATAC experiments'
   author = 'Vladimir Shitov'
 }
diff --git a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml
index 5bb6523c..e9fdc238 100644
--- a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml
+++ b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_mkfastq"
 namespace: "demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -228,11 +228,11 @@ build_info:
   output: "target/nextflow/demux/cellranger_mkfastq"
   executable: "target/nextflow/demux/cellranger_mkfastq/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -262,7 +262,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/demux/cellranger_mkfastq/main.nf b/target/nextflow/demux/cellranger_mkfastq/main.nf
index 7cbfcdc8..c2d5fff8 100644
--- a/target/nextflow/demux/cellranger_mkfastq/main.nf
+++ b/target/nextflow/demux/cellranger_mkfastq/main.nf
@@ -1,4 +1,4 @@
-// cellranger_mkfastq v4.0.0
+// cellranger_mkfastq v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_mkfastq",
   "namespace" : "demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3306,7 +3306,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/cellranger:9.0",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3338,12 +3338,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/demux/cellranger_mkfastq",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3368,7 +3368,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3859,7 +3859,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/demux/cellranger_mkfastq",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/demux/cellranger_mkfastq/nextflow.config b/target/nextflow/demux/cellranger_mkfastq/nextflow.config
index acb03f8b..8f7ec5be 100644
--- a/target/nextflow/demux/cellranger_mkfastq/nextflow.config
+++ b/target/nextflow/demux/cellranger_mkfastq/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'demux/cellranger_mkfastq'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Demultiplex raw sequencing data'
   author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml b/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml
index 1be48a64..7bf8bd54 100644
--- a/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml
+++ b/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "create_pseudobulk"
 namespace: "differential_expression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -271,7 +271,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -309,11 +309,11 @@ build_info:
   output: "target/nextflow/differential_expression/create_pseudobulk"
   executable: "target/nextflow/differential_expression/create_pseudobulk/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -343,7 +343,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/differential_expression/create_pseudobulk/main.nf b/target/nextflow/differential_expression/create_pseudobulk/main.nf
index c82c7f7b..6b6912f2 100644
--- a/target/nextflow/differential_expression/create_pseudobulk/main.nf
+++ b/target/nextflow/differential_expression/create_pseudobulk/main.nf
@@ -1,4 +1,4 @@
-// create_pseudobulk v4.0.0
+// create_pseudobulk v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3038,7 +3038,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_pseudobulk",
   "namespace" : "differential_expression",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3386,7 +3386,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3436,12 +3436,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/differential_expression/create_pseudobulk",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3466,7 +3466,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3996,7 +3996,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/differential_expression/create_pseudobulk",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/differential_expression/create_pseudobulk/nextflow.config b/target/nextflow/differential_expression/create_pseudobulk/nextflow.config
index d2c7183d..45bb5115 100644
--- a/target/nextflow/differential_expression/create_pseudobulk/nextflow.config
+++ b/target/nextflow/differential_expression/create_pseudobulk/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'differential_expression/create_pseudobulk'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Generation of pseudobulk samples from single-cell transcriptomics data,\nby aggregating raw gene expression counts from individual cells to create \nbulk-like expression profiles suitable for differential expression analysis\nwith methods designed for bulk differential expression analysis.\nNote that this componentonly considers factors as explanatory variables, \nand excludes covariates from the analysis.\n'
   author = 'Dorien Roosen, Jakub Majercik, Dries De Maeyer, Weiwei Schultz'
 }
diff --git a/target/nextflow/differential_expression/deseq2/.config.vsh.yaml b/target/nextflow/differential_expression/deseq2/.config.vsh.yaml
index 80b9cba1..cb340b35 100644
--- a/target/nextflow/differential_expression/deseq2/.config.vsh.yaml
+++ b/target/nextflow/differential_expression/deseq2/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "deseq2"
 namespace: "differential_expression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -294,7 +294,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -346,11 +346,11 @@ build_info:
   output: "target/nextflow/differential_expression/deseq2"
   executable: "target/nextflow/differential_expression/deseq2/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -380,7 +380,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/differential_expression/deseq2/main.nf b/target/nextflow/differential_expression/deseq2/main.nf
index 82b8be0b..3caf80e6 100644
--- a/target/nextflow/differential_expression/deseq2/main.nf
+++ b/target/nextflow/differential_expression/deseq2/main.nf
@@ -1,4 +1,4 @@
-// deseq2 v4.0.0
+// deseq2 v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3038,7 +3038,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "deseq2",
   "namespace" : "differential_expression",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3399,7 +3399,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3475,12 +3475,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/differential_expression/deseq2",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3505,7 +3505,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4350,7 +4350,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/differential_expression/deseq2",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/differential_expression/deseq2/nextflow.config b/target/nextflow/differential_expression/deseq2/nextflow.config
index 2d4230a0..15d54314 100644
--- a/target/nextflow/differential_expression/deseq2/nextflow.config
+++ b/target/nextflow/differential_expression/deseq2/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'differential_expression/deseq2'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs differential expression analysis using DESeq2 on bulk samples or pseudobulk samples aggregated from single-cell data.\nNote that this component only considers factors as explanatory variables, and excludes covariates from the analysis.\n'
   author = 'Jakub Majercik, Dorien Roosen, Dries De Maeyer, Weiwei Schultz'
 }
diff --git a/target/nextflow/dimred/densmap/.config.vsh.yaml b/target/nextflow/dimred/densmap/.config.vsh.yaml
index b7a62a95..5d005f57 100644
--- a/target/nextflow/dimred/densmap/.config.vsh.yaml
+++ b/target/nextflow/dimred/densmap/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "densmap"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -353,7 +353,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -395,11 +395,11 @@ build_info:
   output: "target/nextflow/dimred/densmap"
   executable: "target/nextflow/dimred/densmap/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -429,7 +429,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dimred/densmap/main.nf b/target/nextflow/dimred/densmap/main.nf
index 215fee2a..b3d700b1 100644
--- a/target/nextflow/dimred/densmap/main.nf
+++ b/target/nextflow/dimred/densmap/main.nf
@@ -1,4 +1,4 @@
-// densmap v4.0.0
+// densmap v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "densmap",
   "namespace" : "dimred",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3449,7 +3449,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3506,12 +3506,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dimred/densmap",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3536,7 +3536,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4076,7 +4076,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dimred/densmap",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/dimred/densmap/nextflow.config b/target/nextflow/dimred/densmap/nextflow.config
index 5649205d..249ef102 100644
--- a/target/nextflow/dimred/densmap/nextflow.config
+++ b/target/nextflow/dimred/densmap/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dimred/densmap'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'A modification of UMAP that adds an extra cost term in order to preserve information \nabout the relative local density of the data. It is performed on the same inputs as UMAP.\n'
   author = 'Jakub Majercik'
 }
diff --git a/target/nextflow/dimred/lsi/.config.vsh.yaml b/target/nextflow/dimred/lsi/.config.vsh.yaml
index 82c24d62..374f189c 100644
--- a/target/nextflow/dimred/lsi/.config.vsh.yaml
+++ b/target/nextflow/dimred/lsi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "lsi"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Sarah Ouologuem"
   roles:
@@ -269,7 +269,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -314,11 +314,11 @@ build_info:
   output: "target/nextflow/dimred/lsi"
   executable: "target/nextflow/dimred/lsi/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -348,7 +348,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dimred/lsi/main.nf b/target/nextflow/dimred/lsi/main.nf
index 8a35a191..84189277 100644
--- a/target/nextflow/dimred/lsi/main.nf
+++ b/target/nextflow/dimred/lsi/main.nf
@@ -1,4 +1,4 @@
-// lsi v4.0.0
+// lsi v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "lsi",
   "namespace" : "dimred",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Sarah Ouologuem",
@@ -3383,7 +3383,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3443,12 +3443,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dimred/lsi",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3473,7 +3473,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4023,7 +4023,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dimred/lsi",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/dimred/lsi/nextflow.config b/target/nextflow/dimred/lsi/nextflow.config
index 54b77bec..f3a6597e 100644
--- a/target/nextflow/dimred/lsi/nextflow.config
+++ b/target/nextflow/dimred/lsi/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dimred/lsi'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and singular values. Uses the implementation of scipy.\n'
   author = 'Sarah Ouologuem, Vladimir Shitov'
 }
diff --git a/target/nextflow/dimred/pca/.config.vsh.yaml b/target/nextflow/dimred/pca/.config.vsh.yaml
index cab800a2..99356f04 100644
--- a/target/nextflow/dimred/pca/.config.vsh.yaml
+++ b/target/nextflow/dimred/pca/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "pca"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -240,7 +240,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -276,11 +276,11 @@ build_info:
   output: "target/nextflow/dimred/pca"
   executable: "target/nextflow/dimred/pca/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -310,7 +310,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dimred/pca/main.nf b/target/nextflow/dimred/pca/main.nf
index 07a8b5dc..74ddbccc 100644
--- a/target/nextflow/dimred/pca/main.nf
+++ b/target/nextflow/dimred/pca/main.nf
@@ -1,4 +1,4 @@
-// pca v4.0.0
+// pca v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "pca",
   "namespace" : "dimred",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3333,7 +3333,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3380,12 +3380,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dimred/pca",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3410,7 +3410,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3933,7 +3933,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dimred/pca",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/dimred/pca/nextflow.config b/target/nextflow/dimred/pca/nextflow.config
index 59a4a55d..87744c8c 100644
--- a/target/nextflow/dimred/pca/nextflow.config
+++ b/target/nextflow/dimred/pca/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dimred/pca'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa11].\n'
   author = 'Dries De Maeyer'
 }
diff --git a/target/nextflow/dimred/tsne/.config.vsh.yaml b/target/nextflow/dimred/tsne/.config.vsh.yaml
index ecaeb440..9c4cfdd9 100644
--- a/target/nextflow/dimred/tsne/.config.vsh.yaml
+++ b/target/nextflow/dimred/tsne/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tsne"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -281,7 +281,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -323,11 +323,11 @@ build_info:
   output: "target/nextflow/dimred/tsne"
   executable: "target/nextflow/dimred/tsne/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -357,7 +357,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dimred/tsne/main.nf b/target/nextflow/dimred/tsne/main.nf
index 9bdc3ac8..eb62110e 100644
--- a/target/nextflow/dimred/tsne/main.nf
+++ b/target/nextflow/dimred/tsne/main.nf
@@ -1,4 +1,4 @@
-// tsne v4.0.0
+// tsne v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "tsne",
   "namespace" : "dimred",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3373,7 +3373,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3430,12 +3430,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dimred/tsne",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3460,7 +3460,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3964,7 +3964,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dimred/tsne",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/dimred/tsne/nextflow.config b/target/nextflow/dimred/tsne/nextflow.config
index 20de8c76..97421139 100644
--- a/target/nextflow/dimred/tsne/nextflow.config
+++ b/target/nextflow/dimred/tsne/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dimred/tsne'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 't-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality reduction technique used to visualize high-dimensional data in a low-dimensional space, revealing patterns and clusters by preserving local data similarities.\n'
   author = 'Jakub Majercik'
 }
diff --git a/target/nextflow/dimred/umap/.config.vsh.yaml b/target/nextflow/dimred/umap/.config.vsh.yaml
index 32cdaa90..7bf49dab 100644
--- a/target/nextflow/dimred/umap/.config.vsh.yaml
+++ b/target/nextflow/dimred/umap/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "umap"
 namespace: "dimred"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -294,7 +294,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -330,11 +330,11 @@ build_info:
   output: "target/nextflow/dimred/umap"
   executable: "target/nextflow/dimred/umap/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -364,7 +364,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/dimred/umap/main.nf b/target/nextflow/dimred/umap/main.nf
index 6e3e3fc8..fc795e69 100644
--- a/target/nextflow/dimred/umap/main.nf
+++ b/target/nextflow/dimred/umap/main.nf
@@ -1,4 +1,4 @@
-// umap v4.0.0
+// umap v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "umap",
   "namespace" : "dimred",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3382,7 +3382,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3429,12 +3429,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dimred/umap",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3459,7 +3459,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3971,7 +3971,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/dimred/umap",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/dimred/umap/nextflow.config b/target/nextflow/dimred/umap/nextflow.config
index 008fca3e..67b7637f 100644
--- a/target/nextflow/dimred/umap/nextflow.config
+++ b/target/nextflow/dimred/umap/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'dimred/umap'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data. Besides tending to be faster than tSNE, it optimizes the embedding such that it best reflects the topology of the data, which we represent throughout Scanpy using a neighborhood graph. tSNE, by contrast, optimizes the distribution of nearest-neighbor distances in the embedding such that these best match the distribution of distances in the high-dimensional space. We use the implementation of umap-learn [McInnes18]. For a few comparisons of UMAP with tSNE, see this preprint.\n'
   author = 'Dries De Maeyer'
 }
diff --git a/target/nextflow/download/download_file/.config.vsh.yaml b/target/nextflow/download/download_file/.config.vsh.yaml
index 8797958e..b1aa7101 100644
--- a/target/nextflow/download/download_file/.config.vsh.yaml
+++ b/target/nextflow/download/download_file/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "download_file"
 namespace: "download"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -146,7 +146,7 @@ engines:
   id: "docker"
   image: "bash:5.1.16"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -159,11 +159,11 @@ build_info:
   output: "target/nextflow/download/download_file"
   executable: "target/nextflow/download/download_file/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -193,7 +193,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/download/download_file/main.nf b/target/nextflow/download/download_file/main.nf
index 9556f8eb..e985e081 100644
--- a/target/nextflow/download/download_file/main.nf
+++ b/target/nextflow/download/download_file/main.nf
@@ -1,4 +1,4 @@
-// download_file v4.0.0
+// download_file v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "download_file",
   "namespace" : "download",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3221,7 +3221,7 @@ meta = [
       "id" : "docker",
       "image" : "bash:5.1.16",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/"
     },
     {
@@ -3235,12 +3235,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/download/download_file",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3265,7 +3265,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3712,7 +3712,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/download/download_file",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/download/download_file/nextflow.config b/target/nextflow/download/download_file/nextflow.config
index 3ca622f1..282abd60 100644
--- a/target/nextflow/download/download_file/nextflow.config
+++ b/target/nextflow/download/download_file/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'download/download_file'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Download a file.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml b/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml
index 24f01861..cd539778 100644
--- a/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml
+++ b/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "align_query_reference"
 namespace: "feature_annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -476,7 +476,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -517,11 +517,11 @@ build_info:
   output: "target/nextflow/feature_annotation/align_query_reference"
   executable: "target/nextflow/feature_annotation/align_query_reference/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -551,7 +551,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/feature_annotation/align_query_reference/main.nf b/target/nextflow/feature_annotation/align_query_reference/main.nf
index 33d50ded..01a9aac4 100644
--- a/target/nextflow/feature_annotation/align_query_reference/main.nf
+++ b/target/nextflow/feature_annotation/align_query_reference/main.nf
@@ -1,4 +1,4 @@
-// align_query_reference v4.0.0
+// align_query_reference v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "align_query_reference",
   "namespace" : "feature_annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3583,7 +3583,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3639,12 +3639,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/feature_annotation/align_query_reference",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3669,7 +3669,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4399,7 +4399,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/feature_annotation/align_query_reference",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/feature_annotation/align_query_reference/nextflow.config b/target/nextflow/feature_annotation/align_query_reference/nextflow.config
index 1d87e5df..d27bb3cf 100644
--- a/target/nextflow/feature_annotation/align_query_reference/nextflow.config
+++ b/target/nextflow/feature_annotation/align_query_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'feature_annotation/align_query_reference'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Alignment of a query and reference dataset by:\n* Alignment of layers\n* Harmonization of .obs field names for batch and cell type labels\n* Harmonization of .var field name for gene names\n* Sanitation of gene names\n* Cross-checking of genes\n* Assignment of an id to the query and reference datasets\n'
   author = 'Dorien Roosen'
 }
diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml b/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml
index ca1929b4..0049ddb5 100644
--- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml
+++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "highly_variable_features_scanpy"
 namespace: "feature_annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -342,7 +342,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -381,11 +381,11 @@ build_info:
   output: "target/nextflow/feature_annotation/highly_variable_features_scanpy"
   executable: "target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -415,7 +415,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf b/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf
index 064d7174..53c6419a 100644
--- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf
+++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf
@@ -1,4 +1,4 @@
-// highly_variable_features_scanpy v4.0.0
+// highly_variable_features_scanpy v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "highly_variable_features_scanpy",
   "namespace" : "feature_annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3430,7 +3430,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3481,12 +3481,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/feature_annotation/highly_variable_features_scanpy",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3511,7 +3511,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4110,7 +4110,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/feature_annotation/highly_variable_features_scanpy",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config b/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config
index 22968acf..d5696168 100644
--- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config
+++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'feature_annotation/highly_variable_features_scanpy'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Annotate highly variable features [Satija15] [Zheng17] [Stuart19].\n\nExpects logarithmized data, except when flavor=\'seurat_v3\' in which count data is expected.\n\nDepending on flavor, this reproduces the R-implementations of Seurat [Satija15], Cell Ranger [Zheng17], and Seurat v3 [Stuart19].\n\nFor the dispersion-based methods ([Satija15] and [Zheng17]), the normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for features falling into a given bin for mean expression of features. This means that for each bin of mean expression, highly variable features are selected.\n\nFor [Stuart19], a normalized variance for each feature is computed. First, the data are standardized (i.e., z-score normalization per feature) with a regularized standard deviation. Next, the normalized variance is computed as the variance of each feature after the transformation. Features are ranked by the normalized variance.\n'
   author = 'Dries De Maeyer, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml
index c5a324f0..d61a317d 100644
--- a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml
+++ b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "score_genes_cell_cycle_scanpy"
 namespace: "feature_annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -367,7 +367,7 @@ engines:
   id: "docker"
   image: "python:3.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -399,11 +399,11 @@ build_info:
   output: "target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy"
   executable: "target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -433,7 +433,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf
index 2bd82936..8cca1119 100644
--- a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf
+++ b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf
@@ -1,4 +1,4 @@
-// score_genes_cell_cycle_scanpy v4.0.0
+// score_genes_cell_cycle_scanpy v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "score_genes_cell_cycle_scanpy",
   "namespace" : "feature_annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3484,7 +3484,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3524,12 +3524,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3554,7 +3554,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4085,7 +4085,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/feature_annotation/score_genes_cell_cycle_scanpy",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config
index dd83fb6b..f378e5e1 100644
--- a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config
+++ b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'feature_annotation/score_genes_cell_cycle_scanpy'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Calculates the score associated to S phase and G2M phase and annotates the cell cycle phase for each cell, as implemented by scanpy. \nThe score is the average expression of a set of genes subtracted with the average expression of a reference set of genes.\n'
   author = 'Robrecht Cannoodt, Dorien Roosen, Weiwei Schultz'
 }
diff --git a/target/nextflow/files/make_params/.config.vsh.yaml b/target/nextflow/files/make_params/.config.vsh.yaml
index b50479b8..64a5a0f8 100644
--- a/target/nextflow/files/make_params/.config.vsh.yaml
+++ b/target/nextflow/files/make_params/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "make_params"
 namespace: "files"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -223,7 +223,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/randpy:r4.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -236,11 +236,11 @@ build_info:
   output: "target/nextflow/files/make_params"
   executable: "target/nextflow/files/make_params/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -270,7 +270,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/files/make_params/main.nf b/target/nextflow/files/make_params/main.nf
index 35821876..40b455a9 100644
--- a/target/nextflow/files/make_params/main.nf
+++ b/target/nextflow/files/make_params/main.nf
@@ -1,4 +1,4 @@
-// make_params v4.0.0
+// make_params v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "make_params",
   "namespace" : "files",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3321,7 +3321,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/randpy:r4.0",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/"
     },
     {
@@ -3335,12 +3335,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/files/make_params",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3365,7 +3365,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3881,7 +3881,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/files/make_params",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/files/make_params/nextflow.config b/target/nextflow/files/make_params/nextflow.config
index 5ce573ef..17400274 100644
--- a/target/nextflow/files/make_params/nextflow.config
+++ b/target/nextflow/files/make_params/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'files/make_params'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Looks for files in a directory and turn it in a params file.'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml
index 6ef9b532..1b073fa5 100644
--- a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml
+++ b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "delimit_fraction"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -219,7 +219,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -260,11 +260,11 @@ build_info:
   output: "target/nextflow/filter/delimit_fraction"
   executable: "target/nextflow/filter/delimit_fraction/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -294,7 +294,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/delimit_fraction/main.nf b/target/nextflow/filter/delimit_fraction/main.nf
index b0981582..3ce02f81 100644
--- a/target/nextflow/filter/delimit_fraction/main.nf
+++ b/target/nextflow/filter/delimit_fraction/main.nf
@@ -1,4 +1,4 @@
-// delimit_fraction v4.0.0
+// delimit_fraction v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "delimit_fraction",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3312,7 +3312,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3368,12 +3368,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/delimit_fraction",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3398,7 +3398,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3928,7 +3928,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/delimit_fraction",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/filter/delimit_fraction/nextflow.config b/target/nextflow/filter/delimit_fraction/nextflow.config
index 6b0447a7..973dd925 100644
--- a/target/nextflow/filter/delimit_fraction/nextflow.config
+++ b/target/nextflow/filter/delimit_fraction/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/delimit_fraction'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Turns a column containing values between 0 and 1 into a boolean column based on thresholds.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/filter/do_filter/.config.vsh.yaml b/target/nextflow/filter/do_filter/.config.vsh.yaml
index 86bad073..bf2bf738 100644
--- a/target/nextflow/filter/do_filter/.config.vsh.yaml
+++ b/target/nextflow/filter/do_filter/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "do_filter"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -193,7 +193,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -228,11 +228,11 @@ build_info:
   output: "target/nextflow/filter/do_filter"
   executable: "target/nextflow/filter/do_filter/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -262,7 +262,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/do_filter/main.nf b/target/nextflow/filter/do_filter/main.nf
index 89c6758a..2f4a45f8 100644
--- a/target/nextflow/filter/do_filter/main.nf
+++ b/target/nextflow/filter/do_filter/main.nf
@@ -1,4 +1,4 @@
-// do_filter v4.0.0
+// do_filter v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "do_filter",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3282,7 +3282,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3328,12 +3328,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/do_filter",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3358,7 +3358,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3851,7 +3851,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/do_filter",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/filter/do_filter/nextflow.config b/target/nextflow/filter/do_filter/nextflow.config
index 17c11f1f..cea4cbbb 100644
--- a/target/nextflow/filter/do_filter/nextflow.config
+++ b/target/nextflow/filter/do_filter/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/do_filter'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Remove observations and variables based on specified .obs and .var columns.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml
index 089d6a4d..9b46a06f 100644
--- a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml
+++ b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_with_counts"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -280,7 +280,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -321,11 +321,11 @@ build_info:
   output: "target/nextflow/filter/filter_with_counts"
   executable: "target/nextflow/filter/filter_with_counts/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -355,7 +355,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/filter_with_counts/main.nf b/target/nextflow/filter/filter_with_counts/main.nf
index 0452c27f..b4d1a98a 100644
--- a/target/nextflow/filter/filter_with_counts/main.nf
+++ b/target/nextflow/filter/filter_with_counts/main.nf
@@ -1,4 +1,4 @@
-// filter_with_counts v4.0.0
+// filter_with_counts v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "filter_with_counts",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3392,7 +3392,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3448,12 +3448,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/filter_with_counts",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3478,7 +3478,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4050,7 +4050,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/filter_with_counts",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/filter/filter_with_counts/nextflow.config b/target/nextflow/filter/filter_with_counts/nextflow.config
index 67320157..648e1c81 100644
--- a/target/nextflow/filter/filter_with_counts/nextflow.config
+++ b/target/nextflow/filter/filter_with_counts/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/filter_with_counts'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Filter scRNA-seq data based on the primary QC metrics. \nThis is based on both the UMI counts, the gene counts \nand the mitochondrial genes (genes starting with mt/MT).\n'
   author = 'Dries De Maeyer, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml b/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml
index bf0e9f44..12c15ce3 100644
--- a/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml
+++ b/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_with_pattern"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -211,7 +211,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -246,11 +246,11 @@ build_info:
   output: "target/nextflow/filter/filter_with_pattern"
   executable: "target/nextflow/filter/filter_with_pattern/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/filter_with_pattern/main.nf b/target/nextflow/filter/filter_with_pattern/main.nf
index e125d113..5942e113 100644
--- a/target/nextflow/filter/filter_with_pattern/main.nf
+++ b/target/nextflow/filter/filter_with_pattern/main.nf
@@ -1,4 +1,4 @@
-// filter_with_pattern v4.0.0
+// filter_with_pattern v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "filter_with_pattern",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3302,7 +3302,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3348,12 +3348,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/filter_with_pattern",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3378,7 +3378,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3877,7 +3877,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/filter_with_pattern",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/filter/filter_with_pattern/nextflow.config b/target/nextflow/filter/filter_with_pattern/nextflow.config
index 281ca952..70692eaa 100644
--- a/target/nextflow/filter/filter_with_pattern/nextflow.config
+++ b/target/nextflow/filter/filter_with_pattern/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/filter_with_pattern'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Filter a MuData object based on gene names using a regex.\n'
   author = 'Dorien Roosen'
 }
diff --git a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml
index c8c0a7a0..72e1a60d 100644
--- a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml
+++ b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_with_scrublet"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -333,7 +333,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -378,11 +378,11 @@ build_info:
   output: "target/nextflow/filter/filter_with_scrublet"
   executable: "target/nextflow/filter/filter_with_scrublet/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -412,7 +412,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/filter_with_scrublet/main.nf b/target/nextflow/filter/filter_with_scrublet/main.nf
index c1bc1392..ad550566 100644
--- a/target/nextflow/filter/filter_with_scrublet/main.nf
+++ b/target/nextflow/filter/filter_with_scrublet/main.nf
@@ -1,4 +1,4 @@
-// filter_with_scrublet v4.0.0
+// filter_with_scrublet v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "filter_with_scrublet",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3429,7 +3429,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3489,12 +3489,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/filter_with_scrublet",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3519,7 +3519,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4065,7 +4065,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/filter_with_scrublet",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highcpu",
diff --git a/target/nextflow/filter/filter_with_scrublet/nextflow.config b/target/nextflow/filter/filter_with_scrublet/nextflow.config
index dd320d5d..dab10088 100644
--- a/target/nextflow/filter/filter_with_scrublet/nextflow.config
+++ b/target/nextflow/filter/filter_with_scrublet/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/filter_with_scrublet'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019).\nThe method tests for potential doublets by using the expression profiles of\ncells to generate synthetic potential doubles which are tested against cells. \nThe method returns a "doublet score" on which it calls for potential doublets.\n\nFor the source code please visit https://github.com/AllonKleinLab/scrublet.\n\nFor 10x we expect the doublet rates to be:\n  Multiplet Rate (%) - # of Cells Loaded - # of Cells Recovered\n  ~0.4% ~800 ~500\n  ~0.8% ~1,600 ~1,000\n  ~1.6% ~3,200 ~2,000\n  ~2.3% ~4,800 ~3,000\n  ~3.1% ~6,400 ~4,000\n  ~3.9% ~8,000 ~5,000\n  ~4.6% ~9,600 ~6,000\n  ~5.4% ~11,200 ~7,000\n  ~6.1% ~12,800 ~8,000\n  ~6.9% ~14,400 ~9,000\n  ~7.6% ~16,000 ~10,000\n'
   author = 'Dries De Maeyer, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/filter/intersect_obs/.config.vsh.yaml b/target/nextflow/filter/intersect_obs/.config.vsh.yaml
index 3b6db7a8..1272f152 100644
--- a/target/nextflow/filter/intersect_obs/.config.vsh.yaml
+++ b/target/nextflow/filter/intersect_obs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "intersect_obs"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -183,7 +183,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -218,11 +218,11 @@ build_info:
   output: "target/nextflow/filter/intersect_obs"
   executable: "target/nextflow/filter/intersect_obs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -252,7 +252,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/intersect_obs/main.nf b/target/nextflow/filter/intersect_obs/main.nf
index 07c874e8..716919ce 100644
--- a/target/nextflow/filter/intersect_obs/main.nf
+++ b/target/nextflow/filter/intersect_obs/main.nf
@@ -1,4 +1,4 @@
-// intersect_obs v4.0.0
+// intersect_obs v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "intersect_obs",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3274,7 +3274,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3320,12 +3320,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/intersect_obs",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3350,7 +3350,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3857,7 +3857,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/intersect_obs",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/filter/intersect_obs/nextflow.config b/target/nextflow/filter/intersect_obs/nextflow.config
index 20fb913e..4ed478ad 100644
--- a/target/nextflow/filter/intersect_obs/nextflow.config
+++ b/target/nextflow/filter/intersect_obs/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/intersect_obs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Create an intersection between two or more modalities.\n\nThis component removes any observations which are not present in all modalities.\n'
   author = 'Dries Schaumont, Isabelle Bergiers'
 }
diff --git a/target/nextflow/filter/remove_modality/.config.vsh.yaml b/target/nextflow/filter/remove_modality/.config.vsh.yaml
index b3e2cd75..0192d113 100644
--- a/target/nextflow/filter/remove_modality/.config.vsh.yaml
+++ b/target/nextflow/filter/remove_modality/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "remove_modality"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -163,7 +163,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -198,11 +198,11 @@ build_info:
   output: "target/nextflow/filter/remove_modality"
   executable: "target/nextflow/filter/remove_modality/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -232,7 +232,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/remove_modality/main.nf b/target/nextflow/filter/remove_modality/main.nf
index d0fcc235..2675bef8 100644
--- a/target/nextflow/filter/remove_modality/main.nf
+++ b/target/nextflow/filter/remove_modality/main.nf
@@ -1,4 +1,4 @@
-// remove_modality v4.0.0
+// remove_modality v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "remove_modality",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3241,7 +3241,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3287,12 +3287,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/remove_modality",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3317,7 +3317,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3774,7 +3774,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/remove_modality",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/filter/remove_modality/nextflow.config b/target/nextflow/filter/remove_modality/nextflow.config
index df561cc7..29cdea4f 100644
--- a/target/nextflow/filter/remove_modality/nextflow.config
+++ b/target/nextflow/filter/remove_modality/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/remove_modality'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Remove a modality from a .h5mu file\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml
index c31169a7..374cb0cd 100644
--- a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml
+++ b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "subset_h5mu"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -177,7 +177,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -212,11 +212,11 @@ build_info:
   output: "target/nextflow/filter/subset_h5mu"
   executable: "target/nextflow/filter/subset_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -246,7 +246,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/subset_h5mu/main.nf b/target/nextflow/filter/subset_h5mu/main.nf
index a288080f..411bc4a7 100644
--- a/target/nextflow/filter/subset_h5mu/main.nf
+++ b/target/nextflow/filter/subset_h5mu/main.nf
@@ -1,4 +1,4 @@
-// subset_h5mu v4.0.0
+// subset_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "subset_h5mu",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3260,7 +3260,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3306,12 +3306,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/subset_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3336,7 +3336,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3797,7 +3797,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/subset_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/filter/subset_h5mu/nextflow.config b/target/nextflow/filter/subset_h5mu/nextflow.config
index 415b48b4..665eb90a 100644
--- a/target/nextflow/filter/subset_h5mu/nextflow.config
+++ b/target/nextflow/filter/subset_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/subset_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Create a subset of a mudata file by selecting the first number of observations\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/filter/subset_obsp/.config.vsh.yaml b/target/nextflow/filter/subset_obsp/.config.vsh.yaml
index 6d21628c..6bbded93 100644
--- a/target/nextflow/filter/subset_obsp/.config.vsh.yaml
+++ b/target/nextflow/filter/subset_obsp/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "subset_obsp"
 namespace: "filter"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -207,7 +207,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -248,11 +248,11 @@ build_info:
   output: "target/nextflow/filter/subset_obsp"
   executable: "target/nextflow/filter/subset_obsp/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -282,7 +282,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/filter/subset_obsp/main.nf b/target/nextflow/filter/subset_obsp/main.nf
index 392a6a59..7d71c4a3 100644
--- a/target/nextflow/filter/subset_obsp/main.nf
+++ b/target/nextflow/filter/subset_obsp/main.nf
@@ -1,4 +1,4 @@
-// subset_obsp v4.0.0
+// subset_obsp v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "subset_obsp",
   "namespace" : "filter",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3298,7 +3298,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3354,12 +3354,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/filter/subset_obsp",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3384,7 +3384,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3872,7 +3872,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/filter/subset_obsp",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/filter/subset_obsp/nextflow.config b/target/nextflow/filter/subset_obsp/nextflow.config
index 3eaa1687..e2bba2cd 100644
--- a/target/nextflow/filter/subset_obsp/nextflow.config
+++ b/target/nextflow/filter/subset_obsp/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'filter/subset_obsp'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Create a subset of an .obsp field in a mudata file, by filtering the columns based on the values of an .obs column. The resulting subset is moved to an .obsm slot.\n'
   author = 'Dorien Roosen'
 }
diff --git a/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml b/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml
index f2f94dd1..d4f1befb 100644
--- a/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bcftools"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -195,11 +195,11 @@ build_info:
   output: "target/nextflow/genetic_demux/bcftools"
   executable: "target/nextflow/genetic_demux/bcftools/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -229,7 +229,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/bcftools/main.nf b/target/nextflow/genetic_demux/bcftools/main.nf
index b4814c31..caa6d63f 100644
--- a/target/nextflow/genetic_demux/bcftools/main.nf
+++ b/target/nextflow/genetic_demux/bcftools/main.nf
@@ -1,4 +1,4 @@
-// bcftools v4.0.0
+// bcftools v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bcftools",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3236,7 +3236,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3278,12 +3278,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/bcftools",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3308,7 +3308,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3765,7 +3765,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/bcftools",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/genetic_demux/bcftools/nextflow.config b/target/nextflow/genetic_demux/bcftools/nextflow.config
index 5648cb7a..d85ef813 100644
--- a/target/nextflow/genetic_demux/bcftools/nextflow.config
+++ b/target/nextflow/genetic_demux/bcftools/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/bcftools'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Filter the variants called by freebayes or cellSNP'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml b/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml
index 2f378e3c..c7be5974 100644
--- a/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellsnp"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -327,7 +327,7 @@ engines:
   id: "docker"
   image: "ubuntu:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -369,11 +369,11 @@ build_info:
   output: "target/nextflow/genetic_demux/cellsnp"
   executable: "target/nextflow/genetic_demux/cellsnp/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -403,7 +403,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/cellsnp/main.nf b/target/nextflow/genetic_demux/cellsnp/main.nf
index 9b96f516..38f1edc0 100644
--- a/target/nextflow/genetic_demux/cellsnp/main.nf
+++ b/target/nextflow/genetic_demux/cellsnp/main.nf
@@ -1,4 +1,4 @@
-// cellsnp v4.0.0
+// cellsnp v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellsnp",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3424,7 +3424,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3473,12 +3473,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/cellsnp",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3503,7 +3503,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3993,7 +3993,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/cellsnp",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/genetic_demux/cellsnp/nextflow.config b/target/nextflow/genetic_demux/cellsnp/nextflow.config
index 4a2adecd..097ce677 100644
--- a/target/nextflow/genetic_demux/cellsnp/nextflow.config
+++ b/target/nextflow/genetic_demux/cellsnp/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/cellsnp'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data. It can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo.'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml b/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml
index 045861af..9b8738bf 100644
--- a/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "demuxlet"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -406,7 +406,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -455,11 +455,11 @@ build_info:
   output: "target/nextflow/genetic_demux/demuxlet"
   executable: "target/nextflow/genetic_demux/demuxlet/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -489,7 +489,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/demuxlet/main.nf b/target/nextflow/genetic_demux/demuxlet/main.nf
index 376ad135..c208d2db 100644
--- a/target/nextflow/genetic_demux/demuxlet/main.nf
+++ b/target/nextflow/genetic_demux/demuxlet/main.nf
@@ -1,4 +1,4 @@
-// demuxlet v4.0.0
+// demuxlet v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "demuxlet",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3523,7 +3523,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3584,12 +3584,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/demuxlet",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3614,7 +3614,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4174,7 +4174,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/demuxlet",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/genetic_demux/demuxlet/nextflow.config b/target/nextflow/genetic_demux/demuxlet/nextflow.config
index b7508676..3c8784a0 100644
--- a/target/nextflow/genetic_demux/demuxlet/nextflow.config
+++ b/target/nextflow/genetic_demux/demuxlet/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/demuxlet'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Demuxlet is a software tool to deconvolute sample identity and identify multiplets when\nmultiple samples are pooled by barcoded single cell sequencing. If external genotyping data\nfor each sample is available (e.g. from SNP arrays), demuxlet would be recommended. Be careful\nthat the parameters on the github is not in line with the newest help version.\n'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml b/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml
index 99c2836e..a9bed8e3 100644
--- a/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "dsc_pileup"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -329,7 +329,7 @@ engines:
   id: "docker"
   image: "ubuntu:20.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -367,11 +367,11 @@ build_info:
   output: "target/nextflow/genetic_demux/dsc_pileup"
   executable: "target/nextflow/genetic_demux/dsc_pileup/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -401,7 +401,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/dsc_pileup/main.nf b/target/nextflow/genetic_demux/dsc_pileup/main.nf
index 487bb09a..45cd4cef 100644
--- a/target/nextflow/genetic_demux/dsc_pileup/main.nf
+++ b/target/nextflow/genetic_demux/dsc_pileup/main.nf
@@ -1,4 +1,4 @@
-// dsc_pileup v4.0.0
+// dsc_pileup v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "dsc_pileup",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3432,7 +3432,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:20.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3477,12 +3477,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/dsc_pileup",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3507,7 +3507,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3992,7 +3992,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/dsc_pileup",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/genetic_demux/dsc_pileup/nextflow.config b/target/nextflow/genetic_demux/dsc_pileup/nextflow.config
index d607ba10..f9a5e8c0 100644
--- a/target/nextflow/genetic_demux/dsc_pileup/nextflow.config
+++ b/target/nextflow/genetic_demux/dsc_pileup/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/dsc_pileup'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Dsc-pileup is a software tool to pileup reads and corresponding base quality \nfor each overlapping SNPs and each barcode. By using pileup files,\nit would allow us to run demuxlet/freemuxlet pretty fast multiple times\nwithout going over the BAM file again.\n'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml b/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml
index 55327545..b3713264 100644
--- a/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "freebayes"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -774,7 +774,7 @@ engines:
   id: "docker"
   image: "debian:latest"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -792,11 +792,11 @@ build_info:
   output: "target/nextflow/genetic_demux/freebayes"
   executable: "target/nextflow/genetic_demux/freebayes/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -826,7 +826,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/freebayes/main.nf b/target/nextflow/genetic_demux/freebayes/main.nf
index 54bf1900..9a4d4639 100644
--- a/target/nextflow/genetic_demux/freebayes/main.nf
+++ b/target/nextflow/genetic_demux/freebayes/main.nf
@@ -1,4 +1,4 @@
-// freebayes v4.0.0
+// freebayes v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "freebayes",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3891,7 +3891,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:latest",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3914,12 +3914,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/freebayes",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3944,7 +3944,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4542,7 +4542,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/freebayes",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/genetic_demux/freebayes/nextflow.config b/target/nextflow/genetic_demux/freebayes/nextflow.config
index fc39b173..0ca73915 100644
--- a/target/nextflow/genetic_demux/freebayes/nextflow.config
+++ b/target/nextflow/genetic_demux/freebayes/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/freebayes'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Freebayes is a Bayesian genetic variant detector designed to\nfind small polymorphisms, specifically SNPs.\n'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml b/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml
index 859766d7..dcd20749 100644
--- a/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "freemuxlet"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -322,7 +322,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -371,11 +371,11 @@ build_info:
   output: "target/nextflow/genetic_demux/freemuxlet"
   executable: "target/nextflow/genetic_demux/freemuxlet/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -405,7 +405,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/freemuxlet/main.nf b/target/nextflow/genetic_demux/freemuxlet/main.nf
index c64615b4..37a742a5 100644
--- a/target/nextflow/genetic_demux/freemuxlet/main.nf
+++ b/target/nextflow/genetic_demux/freemuxlet/main.nf
@@ -1,4 +1,4 @@
-// freemuxlet v4.0.0
+// freemuxlet v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "freemuxlet",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3428,7 +3428,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3489,12 +3489,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/freemuxlet",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3519,7 +3519,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4072,7 +4072,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/freemuxlet",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/genetic_demux/freemuxlet/nextflow.config b/target/nextflow/genetic_demux/freemuxlet/nextflow.config
index 94c9c69a..33779a4b 100644
--- a/target/nextflow/genetic_demux/freemuxlet/nextflow.config
+++ b/target/nextflow/genetic_demux/freemuxlet/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/freemuxlet'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Freemuxlet is a software tool to deconvolute sample identity and identify multiplets when\nmultiple samples are pooled by barcoded single cell sequencing. If external genotyping\ndata is not available, the genotyping-free version demuxlet, freemuxlet, would be recommended.\n'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/samtools/.config.vsh.yaml b/target/nextflow/genetic_demux/samtools/.config.vsh.yaml
index 64834601..4a33ad83 100644
--- a/target/nextflow/genetic_demux/samtools/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/samtools/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -138,7 +138,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -173,11 +173,11 @@ build_info:
   output: "target/nextflow/genetic_demux/samtools"
   executable: "target/nextflow/genetic_demux/samtools/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -207,7 +207,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/samtools/main.nf b/target/nextflow/genetic_demux/samtools/main.nf
index b2696846..85cbf737 100644
--- a/target/nextflow/genetic_demux/samtools/main.nf
+++ b/target/nextflow/genetic_demux/samtools/main.nf
@@ -1,4 +1,4 @@
-// samtools v4.0.0
+// samtools v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "samtools",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3212,7 +3212,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3256,12 +3256,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/samtools",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3286,7 +3286,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3730,7 +3730,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/samtools",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/genetic_demux/samtools/nextflow.config b/target/nextflow/genetic_demux/samtools/nextflow.config
index bfaea644..a6e77f84 100644
--- a/target/nextflow/genetic_demux/samtools/nextflow.config
+++ b/target/nextflow/genetic_demux/samtools/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/samtools'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Filter the BAM according to the instruction of scSplit via Samtools.'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml b/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml
index 415360ee..e65dcd3e 100644
--- a/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scsplit"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -265,7 +265,7 @@ engines:
   id: "docker"
   image: "python:3.13"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -301,11 +301,11 @@ build_info:
   output: "target/nextflow/genetic_demux/scsplit"
   executable: "target/nextflow/genetic_demux/scsplit/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -335,7 +335,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/scsplit/main.nf b/target/nextflow/genetic_demux/scsplit/main.nf
index a4c37963..33de5a09 100644
--- a/target/nextflow/genetic_demux/scsplit/main.nf
+++ b/target/nextflow/genetic_demux/scsplit/main.nf
@@ -1,4 +1,4 @@
-// scsplit v4.0.0
+// scsplit v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scsplit",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3355,7 +3355,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3404,12 +3404,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/scsplit",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3434,7 +3434,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3921,7 +3921,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/scsplit",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/genetic_demux/scsplit/nextflow.config b/target/nextflow/genetic_demux/scsplit/nextflow.config
index ff3d9f3b..d7467f4f 100644
--- a/target/nextflow/genetic_demux/scsplit/nextflow.config
+++ b/target/nextflow/genetic_demux/scsplit/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/scsplit'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq, using a hidden state model for identifying genetically distinct samples within a mixed population.'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml b/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml
index b6a14859..02231b4b 100644
--- a/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "souporcell"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -272,7 +272,7 @@ engines:
   id: "docker"
   image: "cumulusprod/souporcell:2022.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   entrypoint: []
   cmd: null
@@ -285,11 +285,11 @@ build_info:
   output: "target/nextflow/genetic_demux/souporcell"
   executable: "target/nextflow/genetic_demux/souporcell/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -319,7 +319,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/souporcell/main.nf b/target/nextflow/genetic_demux/souporcell/main.nf
index 3d704e61..fa9af5bb 100644
--- a/target/nextflow/genetic_demux/souporcell/main.nf
+++ b/target/nextflow/genetic_demux/souporcell/main.nf
@@ -1,4 +1,4 @@
-// souporcell v4.0.0
+// souporcell v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "souporcell",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3362,7 +3362,7 @@ meta = [
       "id" : "docker",
       "image" : "cumulusprod/souporcell:2022.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/"
     },
     {
@@ -3376,12 +3376,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/souporcell",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3406,7 +3406,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3888,7 +3888,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/souporcell",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/genetic_demux/souporcell/nextflow.config b/target/nextflow/genetic_demux/souporcell/nextflow.config
index f96ed01e..c4c09d58 100644
--- a/target/nextflow/genetic_demux/souporcell/nextflow.config
+++ b/target/nextflow/genetic_demux/souporcell/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/souporcell'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/genetic_demux/vireo/.config.vsh.yaml b/target/nextflow/genetic_demux/vireo/.config.vsh.yaml
index 798e4783..b90670e8 100644
--- a/target/nextflow/genetic_demux/vireo/.config.vsh.yaml
+++ b/target/nextflow/genetic_demux/vireo/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "vireo"
 namespace: "genetic_demux"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Xichen Wu"
   roles:
@@ -285,7 +285,7 @@ engines:
   id: "docker"
   image: "python:3.13"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -305,11 +305,11 @@ build_info:
   output: "target/nextflow/genetic_demux/vireo"
   executable: "target/nextflow/genetic_demux/vireo/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -339,7 +339,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/genetic_demux/vireo/main.nf b/target/nextflow/genetic_demux/vireo/main.nf
index 18fd23c8..5f81a577 100644
--- a/target/nextflow/genetic_demux/vireo/main.nf
+++ b/target/nextflow/genetic_demux/vireo/main.nf
@@ -1,4 +1,4 @@
-// vireo v4.0.0
+// vireo v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "vireo",
   "namespace" : "genetic_demux",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Xichen Wu",
@@ -3382,7 +3382,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3407,12 +3407,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/genetic_demux/vireo",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3437,7 +3437,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3921,7 +3921,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/genetic_demux/vireo",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/genetic_demux/vireo/nextflow.config b/target/nextflow/genetic_demux/vireo/nextflow.config
index 5d1bb4a9..8ae33c7f 100644
--- a/target/nextflow/genetic_demux/vireo/nextflow.config
+++ b/target/nextflow/genetic_demux/vireo/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'genetic_demux/vireo'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles.'
   author = 'Xichen Wu'
 }
diff --git a/target/nextflow/integrate/harmonypy/.config.vsh.yaml b/target/nextflow/integrate/harmonypy/.config.vsh.yaml
index b18232a0..c477b328 100644
--- a/target/nextflow/integrate/harmonypy/.config.vsh.yaml
+++ b/target/nextflow/integrate/harmonypy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "harmonypy"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -232,7 +232,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -275,11 +275,11 @@ build_info:
   output: "target/nextflow/integrate/harmonypy"
   executable: "target/nextflow/integrate/harmonypy/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -309,7 +309,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/integrate/harmonypy/main.nf b/target/nextflow/integrate/harmonypy/main.nf
index a335994a..ec839cac 100644
--- a/target/nextflow/integrate/harmonypy/main.nf
+++ b/target/nextflow/integrate/harmonypy/main.nf
@@ -1,4 +1,4 @@
-// harmonypy v4.0.0
+// harmonypy v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "harmonypy",
   "namespace" : "integrate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3330,7 +3330,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3388,12 +3388,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/integrate/harmonypy",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3418,7 +3418,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3904,7 +3904,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/integrate/harmonypy",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/integrate/harmonypy/nextflow.config b/target/nextflow/integrate/harmonypy/nextflow.config
index b02dbd77..812df357 100644
--- a/target/nextflow/integrate/harmonypy/nextflow.config
+++ b/target/nextflow/integrate/harmonypy/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'integrate/harmonypy'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs Harmony integration based as described in https://github.com/immunogenomics/harmony. Based on an implementation in python from https://github.com/slowkow/harmonypy'
   author = 'Dries Schaumont, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/integrate/scanorama/.config.vsh.yaml b/target/nextflow/integrate/scanorama/.config.vsh.yaml
index 2fc4b09c..03d37e1d 100644
--- a/target/nextflow/integrate/scanorama/.config.vsh.yaml
+++ b/target/nextflow/integrate/scanorama/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanorama"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -269,7 +269,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -313,11 +313,11 @@ build_info:
   output: "target/nextflow/integrate/scanorama"
   executable: "target/nextflow/integrate/scanorama/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -347,7 +347,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/integrate/scanorama/main.nf b/target/nextflow/integrate/scanorama/main.nf
index 47d4149c..14978e3e 100644
--- a/target/nextflow/integrate/scanorama/main.nf
+++ b/target/nextflow/integrate/scanorama/main.nf
@@ -1,4 +1,4 @@
-// scanorama v4.0.0
+// scanorama v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scanorama",
   "namespace" : "integrate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3374,7 +3374,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3433,12 +3433,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/integrate/scanorama",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3463,7 +3463,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3957,7 +3957,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/integrate/scanorama",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midcpu",
diff --git a/target/nextflow/integrate/scanorama/nextflow.config b/target/nextflow/integrate/scanorama/nextflow.config
index 40340436..f4969b02 100644
--- a/target/nextflow/integrate/scanorama/nextflow.config
+++ b/target/nextflow/integrate/scanorama/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'integrate/scanorama'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Use Scanorama to integrate different experiments.\n'
   author = 'Dries De Maeyer, Dries Schaumont'
 }
diff --git a/target/nextflow/integrate/scarches/.config.vsh.yaml b/target/nextflow/integrate/scarches/.config.vsh.yaml
index fdde52f5..3b748dab 100644
--- a/target/nextflow/integrate/scarches/.config.vsh.yaml
+++ b/target/nextflow/integrate/scarches/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scarches"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -442,7 +442,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -474,11 +474,11 @@ build_info:
   output: "target/nextflow/integrate/scarches"
   executable: "target/nextflow/integrate/scarches/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -508,7 +508,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/integrate/scarches/main.nf b/target/nextflow/integrate/scarches/main.nf
index 03128d58..06b37666 100644
--- a/target/nextflow/integrate/scarches/main.nf
+++ b/target/nextflow/integrate/scarches/main.nf
@@ -1,4 +1,4 @@
-// scarches v4.0.0
+// scarches v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scarches",
   "namespace" : "integrate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3567,7 +3567,7 @@ meta = [
       "id" : "docker",
       "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3607,12 +3607,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/integrate/scarches",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3637,7 +3637,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4465,7 +4465,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/integrate/scarches",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/integrate/scarches/nextflow.config b/target/nextflow/integrate/scarches/nextflow.config
index a7f531e8..6e5a9b29 100644
--- a/target/nextflow/integrate/scarches/nextflow.config
+++ b/target/nextflow/integrate/scarches/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'integrate/scarches'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs reference mapping with scArches'
   author = 'Vladimir Shitov, Dorien Roosen'
 }
diff --git a/target/nextflow/integrate/scvi/.config.vsh.yaml b/target/nextflow/integrate/scvi/.config.vsh.yaml
index bfcc9f29..fbd0e07e 100644
--- a/target/nextflow/integrate/scvi/.config.vsh.yaml
+++ b/target/nextflow/integrate/scvi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvi"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Malte D. Luecken"
   roles:
@@ -563,7 +563,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -600,11 +600,11 @@ build_info:
   output: "target/nextflow/integrate/scvi"
   executable: "target/nextflow/integrate/scvi/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -634,7 +634,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/integrate/scvi/main.nf b/target/nextflow/integrate/scvi/main.nf
index 1f848e4b..50615866 100644
--- a/target/nextflow/integrate/scvi/main.nf
+++ b/target/nextflow/integrate/scvi/main.nf
@@ -1,4 +1,4 @@
-// scvi v4.0.0
+// scvi v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scvi",
   "namespace" : "integrate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Malte D. Luecken",
@@ -3714,7 +3714,7 @@ meta = [
       "id" : "docker",
       "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3762,12 +3762,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/integrate/scvi",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3792,7 +3792,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4388,7 +4388,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/integrate/scvi",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midcpu",
diff --git a/target/nextflow/integrate/scvi/nextflow.config b/target/nextflow/integrate/scvi/nextflow.config
index 9969b72c..97fc8ea8 100644
--- a/target/nextflow/integrate/scvi/nextflow.config
+++ b/target/nextflow/integrate/scvi/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'integrate/scvi'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs scvi integration as done in the human lung cell atlas https://github.com/LungCellAtlas/HLCA'
   author = 'Malte D. Luecken, Dries Schaumont, Matthias Beyens'
 }
diff --git a/target/nextflow/integrate/totalvi/.config.vsh.yaml b/target/nextflow/integrate/totalvi/.config.vsh.yaml
index 6e6cc5ba..06c91439 100644
--- a/target/nextflow/integrate/totalvi/.config.vsh.yaml
+++ b/target/nextflow/integrate/totalvi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -484,7 +484,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -517,11 +517,11 @@ build_info:
   output: "target/nextflow/integrate/totalvi"
   executable: "target/nextflow/integrate/totalvi/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -551,7 +551,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/integrate/totalvi/main.nf b/target/nextflow/integrate/totalvi/main.nf
index 37d3199b..07a9c971 100644
--- a/target/nextflow/integrate/totalvi/main.nf
+++ b/target/nextflow/integrate/totalvi/main.nf
@@ -1,4 +1,4 @@
-// totalvi v4.0.0
+// totalvi v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "totalvi",
   "namespace" : "integrate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3601,7 +3601,7 @@ meta = [
       "id" : "docker",
       "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3642,12 +3642,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/integrate/totalvi",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3672,7 +3672,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4314,7 +4314,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/integrate/totalvi",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/integrate/totalvi/nextflow.config b/target/nextflow/integrate/totalvi/nextflow.config
index 45de43b4..089dde41 100644
--- a/target/nextflow/integrate/totalvi/nextflow.config
+++ b/target/nextflow/integrate/totalvi/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'integrate/totalvi'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs TotalVI integration of CITE-seq and scRNA-seq data.'
   author = 'Dorien Roosen, Weiwei Schultz'
 }
diff --git a/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml b/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml
index 98655ca1..636afe7a 100644
--- a/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml
+++ b/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi_scarches"
 namespace: "integrate"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   info:
@@ -353,7 +353,7 @@ engines:
   id: "docker"
   image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -385,11 +385,11 @@ build_info:
   output: "target/nextflow/integrate/totalvi_scarches"
   executable: "target/nextflow/integrate/totalvi_scarches/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -419,7 +419,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/integrate/totalvi_scarches/main.nf b/target/nextflow/integrate/totalvi_scarches/main.nf
index abfd6b64..0e8afd2f 100644
--- a/target/nextflow/integrate/totalvi_scarches/main.nf
+++ b/target/nextflow/integrate/totalvi_scarches/main.nf
@@ -1,4 +1,4 @@
-// totalvi_scarches v4.0.0
+// totalvi_scarches v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "totalvi_scarches",
   "namespace" : "integrate",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3457,7 +3457,7 @@ meta = [
       "id" : "docker",
       "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3497,12 +3497,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/integrate/totalvi_scarches",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3527,7 +3527,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4179,7 +4179,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/integrate/totalvi_scarches",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/integrate/totalvi_scarches/nextflow.config b/target/nextflow/integrate/totalvi_scarches/nextflow.config
index b0d94929..33eccfc4 100644
--- a/target/nextflow/integrate/totalvi_scarches/nextflow.config
+++ b/target/nextflow/integrate/totalvi_scarches/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'integrate/totalvi_scarches'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs totalVI integration by mapping the query dataset to a reference dataset or model. \n'
   author = 'Vladimir Shitov'
 }
diff --git a/target/nextflow/interpret/lianapy/.config.vsh.yaml b/target/nextflow/interpret/lianapy/.config.vsh.yaml
index 2d212e15..ca46989a 100644
--- a/target/nextflow/interpret/lianapy/.config.vsh.yaml
+++ b/target/nextflow/interpret/lianapy/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "lianapy"
 namespace: "interpret"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Mauro Saporita"
   roles:
@@ -320,7 +320,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -357,11 +357,11 @@ build_info:
   output: "target/nextflow/interpret/lianapy"
   executable: "target/nextflow/interpret/lianapy/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -391,7 +391,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/interpret/lianapy/main.nf b/target/nextflow/interpret/lianapy/main.nf
index d4d5f7ed..75de9a06 100644
--- a/target/nextflow/interpret/lianapy/main.nf
+++ b/target/nextflow/interpret/lianapy/main.nf
@@ -1,4 +1,4 @@
-// lianapy v4.0.0
+// lianapy v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "lianapy",
   "namespace" : "interpret",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Mauro Saporita",
@@ -3421,7 +3421,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3469,12 +3469,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/interpret/lianapy",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3499,7 +3499,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4020,7 +4020,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/interpret/lianapy",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/interpret/lianapy/nextflow.config b/target/nextflow/interpret/lianapy/nextflow.config
index 120be337..6d9c30ee 100644
--- a/target/nextflow/interpret/lianapy/nextflow.config
+++ b/target/nextflow/interpret/lianapy/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'interpret/lianapy'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs LIANA integration based as described in https://github.com/saezlab/liana-py'
   author = 'Mauro Saporita, Povilas Gibas'
 }
diff --git a/target/nextflow/labels_transfer/knn/.config.vsh.yaml b/target/nextflow/labels_transfer/knn/.config.vsh.yaml
index e6b7351d..715f1a27 100644
--- a/target/nextflow/labels_transfer/knn/.config.vsh.yaml
+++ b/target/nextflow/labels_transfer/knn/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "knn"
 namespace: "labels_transfer"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -406,7 +406,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -455,11 +455,11 @@ build_info:
   output: "target/nextflow/labels_transfer/knn"
   executable: "target/nextflow/labels_transfer/knn/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -489,7 +489,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/labels_transfer/knn/main.nf b/target/nextflow/labels_transfer/knn/main.nf
index 94c035aa..11ab592a 100644
--- a/target/nextflow/labels_transfer/knn/main.nf
+++ b/target/nextflow/labels_transfer/knn/main.nf
@@ -1,4 +1,4 @@
-// knn v4.0.0
+// knn v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "knn",
   "namespace" : "labels_transfer",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3534,7 +3534,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3601,12 +3601,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/labels_transfer/knn",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3631,7 +3631,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4235,7 +4235,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/labels_transfer/knn",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/labels_transfer/knn/nextflow.config b/target/nextflow/labels_transfer/knn/nextflow.config
index 9671ba6e..0b8cd78f 100644
--- a/target/nextflow/labels_transfer/knn/nextflow.config
+++ b/target/nextflow/labels_transfer/knn/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'labels_transfer/knn'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component performs label transfer from reference to query using a K-Neirest Neighbors classifier.\n'
   author = 'Dorien Roosen, Vladimir Shitov'
 }
diff --git a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml
index a98aa2a4..94f380f3 100644
--- a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml
+++ b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "xgboost"
 namespace: "labels_transfer"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -555,7 +555,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -604,11 +604,11 @@ build_info:
   output: "target/nextflow/labels_transfer/xgboost"
   executable: "target/nextflow/labels_transfer/xgboost/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -638,7 +638,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/labels_transfer/xgboost/main.nf b/target/nextflow/labels_transfer/xgboost/main.nf
index 66f9b4e1..0c8ed37e 100644
--- a/target/nextflow/labels_transfer/xgboost/main.nf
+++ b/target/nextflow/labels_transfer/xgboost/main.nf
@@ -1,4 +1,4 @@
-// xgboost v4.0.0
+// xgboost v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "xgboost",
   "namespace" : "labels_transfer",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3697,7 +3697,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3763,12 +3763,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/labels_transfer/xgboost",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3793,7 +3793,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4657,7 +4657,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/labels_transfer/xgboost",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/labels_transfer/xgboost/nextflow.config b/target/nextflow/labels_transfer/xgboost/nextflow.config
index c1c537af..a3a86ae9 100644
--- a/target/nextflow/labels_transfer/xgboost/nextflow.config
+++ b/target/nextflow/labels_transfer/xgboost/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'labels_transfer/xgboost'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs label transfer from reference to query using XGBoost classifier'
   author = 'Vladimir Shitov'
 }
diff --git a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml
index 0e847a75..21b948b1 100644
--- a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml
+++ b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bd_rhapsody"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -1098,7 +1098,7 @@ engines:
   id: "docker"
   image: "bdgenomics/rhapsody:2.2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -1125,11 +1125,11 @@ build_info:
   output: "target/nextflow/mapping/bd_rhapsody"
   executable: "target/nextflow/mapping/bd_rhapsody/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -1159,7 +1159,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/bd_rhapsody/main.nf b/target/nextflow/mapping/bd_rhapsody/main.nf
index bc9a033d..7e2728db 100644
--- a/target/nextflow/mapping/bd_rhapsody/main.nf
+++ b/target/nextflow/mapping/bd_rhapsody/main.nf
@@ -1,4 +1,4 @@
-// bd_rhapsody v4.0.0
+// bd_rhapsody v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bd_rhapsody",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -4399,7 +4399,7 @@ meta = [
       "id" : "docker",
       "image" : "bdgenomics/rhapsody:2.2.1",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -4434,12 +4434,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/bd_rhapsody",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -4464,7 +4464,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -5202,7 +5202,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/bd_rhapsody",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/bd_rhapsody/nextflow.config b/target/nextflow/mapping/bd_rhapsody/nextflow.config
index 39c0c0c4..561f152f 100644
--- a/target/nextflow/mapping/bd_rhapsody/nextflow.config
+++ b/target/nextflow/mapping/bd_rhapsody/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/bd_rhapsody'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'BD Rhapsody Sequence Analysis CWL pipeline v2.2.1\n  \nThis pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported\nsequencing libraries are those generated by the BD Rhapsody assay kits, including: Whole Transcriptome\nmRNA, Targeted mRNA, AbSeq Antibody-Oligonucleotides, Single-Cell Multiplexing, TCR/BCR, and\nATAC-Seq\n\nThe CWL pipeline file is obtained by cloning \'https://bitbucket.org/CRSwDev/cwl\' and removing all objects with class \'DockerRequirement\' from the YAML.\n'
   author = 'Robrecht Cannoodt, Weiwei Schultz'
 }
diff --git a/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml b/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml
index c0a7649f..05a85762 100644
--- a/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml
+++ b/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_atac_count"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -235,7 +235,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger_atac:2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -253,11 +253,11 @@ build_info:
   output: "target/nextflow/mapping/cellranger_atac_count"
   executable: "target/nextflow/mapping/cellranger_atac_count/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -287,7 +287,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/cellranger_atac_count/main.nf b/target/nextflow/mapping/cellranger_atac_count/main.nf
index fdee6172..8a60d7cc 100644
--- a/target/nextflow/mapping/cellranger_atac_count/main.nf
+++ b/target/nextflow/mapping/cellranger_atac_count/main.nf
@@ -1,4 +1,4 @@
-// cellranger_atac_count v4.0.0
+// cellranger_atac_count v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_atac_count",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3324,7 +3324,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/cellranger_atac:2.1",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3346,12 +3346,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_atac_count",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3376,7 +3376,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3892,7 +3892,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/cellranger_atac_count",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/cellranger_atac_count/nextflow.config b/target/nextflow/mapping/cellranger_atac_count/nextflow.config
index a12f4b6a..0cfd0f22 100644
--- a/target/nextflow/mapping/cellranger_atac_count/nextflow.config
+++ b/target/nextflow/mapping/cellranger_atac_count/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/cellranger_atac_count'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Align fastq files using Cell Ranger ATAC count.'
   author = 'Vladimir Shitov'
 }
diff --git a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml
index 436a6bd1..fdaf20d6 100644
--- a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml
+++ b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_count"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -367,7 +367,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -397,11 +397,11 @@ build_info:
   output: "target/nextflow/mapping/cellranger_count"
   executable: "target/nextflow/mapping/cellranger_count/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -431,7 +431,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/cellranger_count/main.nf b/target/nextflow/mapping/cellranger_count/main.nf
index e89ec55b..89a3b270 100644
--- a/target/nextflow/mapping/cellranger_count/main.nf
+++ b/target/nextflow/mapping/cellranger_count/main.nf
@@ -1,4 +1,4 @@
-// cellranger_count v4.0.0
+// cellranger_count v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_count",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3479,7 +3479,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/cellranger:9.0",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3521,12 +3521,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_count",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3551,7 +3551,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4079,7 +4079,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/cellranger_count",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/cellranger_count/nextflow.config b/target/nextflow/mapping/cellranger_count/nextflow.config
index f1205624..36fe6e29 100644
--- a/target/nextflow/mapping/cellranger_count/nextflow.config
+++ b/target/nextflow/mapping/cellranger_count/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/cellranger_count'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Align fastq files using Cell Ranger count.'
   author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml
index 5e94dd75..bf3d3f89 100644
--- a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml
+++ b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_count_split"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -224,7 +224,7 @@ engines:
   id: "docker"
   image: "ubuntu:jammy"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -241,11 +241,11 @@ build_info:
   output: "target/nextflow/mapping/cellranger_count_split"
   executable: "target/nextflow/mapping/cellranger_count_split/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -275,7 +275,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/cellranger_count_split/main.nf b/target/nextflow/mapping/cellranger_count_split/main.nf
index 66b182fa..76c32866 100644
--- a/target/nextflow/mapping/cellranger_count_split/main.nf
+++ b/target/nextflow/mapping/cellranger_count_split/main.nf
@@ -1,4 +1,4 @@
-// cellranger_count_split v4.0.0
+// cellranger_count_split v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_count_split",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3325,7 +3325,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:jammy",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3347,12 +3347,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_count_split",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3377,7 +3377,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3856,7 +3856,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/cellranger_count_split",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/mapping/cellranger_count_split/nextflow.config b/target/nextflow/mapping/cellranger_count_split/nextflow.config
index 3f68b03b..6d72a8b7 100644
--- a/target/nextflow/mapping/cellranger_count_split/nextflow.config
+++ b/target/nextflow/mapping/cellranger_count_split/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/cellranger_count_split'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Split 10x Cell Ranger output directory into separate output fields.'
   author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml
index ac1d49b2..6ddd5347 100644
--- a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml
+++ b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_multi"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -952,7 +952,7 @@ engines:
   id: "docker"
   image: "quay.io/nf-core/cellranger:10.0.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -991,11 +991,11 @@ build_info:
   output: "target/nextflow/mapping/cellranger_multi"
   executable: "target/nextflow/mapping/cellranger_multi/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -1025,7 +1025,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/cellranger_multi/main.nf b/target/nextflow/mapping/cellranger_multi/main.nf
index 3e2af19c..5fe98978 100644
--- a/target/nextflow/mapping/cellranger_multi/main.nf
+++ b/target/nextflow/mapping/cellranger_multi/main.nf
@@ -1,4 +1,4 @@
-// cellranger_multi v4.0.0
+// cellranger_multi v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3040,7 +3040,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_multi",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -4080,7 +4080,7 @@ meta = [
       "id" : "docker",
       "image" : "quay.io/nf-core/cellranger:10.0.0",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -4138,12 +4138,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_multi",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -4168,7 +4168,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -5146,7 +5146,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/cellranger_multi",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "veryhighmem",
diff --git a/target/nextflow/mapping/cellranger_multi/nextflow.config b/target/nextflow/mapping/cellranger_multi/nextflow.config
index e680a137..1c607fbe 100644
--- a/target/nextflow/mapping/cellranger_multi/nextflow.config
+++ b/target/nextflow/mapping/cellranger_multi/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/cellranger_multi'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Align fastq files using Cell Ranger multi.'
   author = 'Dries Schaumont, Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer, Weiwei Schultz, Dorien Roosen'
 }
diff --git a/target/nextflow/mapping/htseq_count/.config.vsh.yaml b/target/nextflow/mapping/htseq_count/.config.vsh.yaml
index f269226d..d8284d4a 100644
--- a/target/nextflow/mapping/htseq_count/.config.vsh.yaml
+++ b/target/nextflow/mapping/htseq_count/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "htseq_count"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -396,7 +396,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -422,11 +422,11 @@ build_info:
   output: "target/nextflow/mapping/htseq_count"
   executable: "target/nextflow/mapping/htseq_count/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -456,7 +456,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/htseq_count/main.nf b/target/nextflow/mapping/htseq_count/main.nf
index 6bec9353..2cf9103a 100644
--- a/target/nextflow/mapping/htseq_count/main.nf
+++ b/target/nextflow/mapping/htseq_count/main.nf
@@ -1,4 +1,4 @@
-// htseq_count v4.0.0
+// htseq_count v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "htseq_count",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3542,7 +3542,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3576,12 +3576,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/htseq_count",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3606,7 +3606,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4181,7 +4181,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/htseq_count",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/htseq_count/nextflow.config b/target/nextflow/mapping/htseq_count/nextflow.config
index e06d2eae..8a6b4a8d 100644
--- a/target/nextflow/mapping/htseq_count/nextflow.config
+++ b/target/nextflow/mapping/htseq_count/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/htseq_count'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Quantify gene expression for subsequent testing for differential expression.\n\nThis script takes one or more alignment files in SAM/BAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. \n\nSee http://htseq.readthedocs.io/en/master/count.html for details.\n'
   author = 'Robrecht Cannoodt, Angela Oliveira Pisco'
 }
diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml
index 69ca2226..a47481db 100644
--- a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "htseq_count_to_h5mu"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -201,7 +201,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -236,11 +236,11 @@ build_info:
   output: "target/nextflow/mapping/htseq_count_to_h5mu"
   executable: "target/nextflow/mapping/htseq_count_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -270,7 +270,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf
index 93b88048..fcaae321 100644
--- a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf
+++ b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// htseq_count_to_h5mu v4.0.0
+// htseq_count_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "htseq_count_to_h5mu",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3299,7 +3299,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3344,12 +3344,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/htseq_count_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3374,7 +3374,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3936,7 +3936,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/htseq_count_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config b/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config
index 2f1f0922..84bc5d4c 100644
--- a/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config
+++ b/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/htseq_count_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert the htseq table to a h5mu.\n'
   author = 'Robrecht Cannoodt, Angela Oliveira Pisco'
 }
diff --git a/target/nextflow/mapping/multi_star/.config.vsh.yaml b/target/nextflow/mapping/multi_star/.config.vsh.yaml
index 4b7a1f93..d5c49ddc 100644
--- a/target/nextflow/mapping/multi_star/.config.vsh.yaml
+++ b/target/nextflow/mapping/multi_star/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "multi_star"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -2856,7 +2856,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -2904,11 +2904,11 @@ build_info:
   output: "target/nextflow/mapping/multi_star"
   executable: "target/nextflow/mapping/multi_star/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -2938,7 +2938,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/multi_star/main.nf b/target/nextflow/mapping/multi_star/main.nf
index dc17de38..d2f165d1 100644
--- a/target/nextflow/mapping/multi_star/main.nf
+++ b/target/nextflow/mapping/multi_star/main.nf
@@ -1,4 +1,4 @@
-// multi_star v4.0.0
+// multi_star v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "multi_star",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -6382,7 +6382,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -6443,12 +6443,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/multi_star",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -6473,7 +6473,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -7554,7 +7554,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/multi_star",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/multi_star/nextflow.config b/target/nextflow/mapping/multi_star/nextflow.config
index a528d53f..28aba388 100644
--- a/target/nextflow/mapping/multi_star/nextflow.config
+++ b/target/nextflow/mapping/multi_star/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/multi_star'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Align fastq files using STAR.'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml
index f3682d29..96e4dc27 100644
--- a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml
+++ b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "multi_star_to_h5mu"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -177,7 +177,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -206,11 +206,11 @@ build_info:
   output: "target/nextflow/mapping/multi_star_to_h5mu"
   executable: "target/nextflow/mapping/multi_star_to_h5mu/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -240,7 +240,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/multi_star_to_h5mu/main.nf b/target/nextflow/mapping/multi_star_to_h5mu/main.nf
index e75c3d85..eb9396c8 100644
--- a/target/nextflow/mapping/multi_star_to_h5mu/main.nf
+++ b/target/nextflow/mapping/multi_star_to_h5mu/main.nf
@@ -1,4 +1,4 @@
-// multi_star_to_h5mu v4.0.0
+// multi_star_to_h5mu v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "multi_star_to_h5mu",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3268,7 +3268,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3304,12 +3304,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/multi_star_to_h5mu",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3334,7 +3334,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3848,7 +3848,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/multi_star_to_h5mu",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config b/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config
index 910c9d84..67dc8e43 100644
--- a/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config
+++ b/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/multi_star_to_h5mu'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert the output of `multi_star` to a h5mu.\n'
   author = 'Robrecht Cannoodt, Angela Oliveira Pisco'
 }
diff --git a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml
index dd900cad..c01ca643 100644
--- a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml
+++ b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools_sort"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -258,7 +258,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -282,11 +282,11 @@ build_info:
   output: "target/nextflow/mapping/samtools_sort"
   executable: "target/nextflow/mapping/samtools_sort/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -316,7 +316,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/samtools_sort/main.nf b/target/nextflow/mapping/samtools_sort/main.nf
index 34a090f3..fff14ae9 100644
--- a/target/nextflow/mapping/samtools_sort/main.nf
+++ b/target/nextflow/mapping/samtools_sort/main.nf
@@ -1,4 +1,4 @@
-// samtools_sort v4.0.0
+// samtools_sort v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "samtools_sort",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3368,7 +3368,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3400,12 +3400,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/samtools_sort",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3430,7 +3430,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3947,7 +3947,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/samtools_sort",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/samtools_sort/nextflow.config b/target/nextflow/mapping/samtools_sort/nextflow.config
index b1b82ccc..75e03634 100644
--- a/target/nextflow/mapping/samtools_sort/nextflow.config
+++ b/target/nextflow/mapping/samtools_sort/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/samtools_sort'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Sort and (optionally) index alignments.\n\nReads are sorted by leftmost coordinates, or by read name when `--sort_by_read_names` is used.\n\nAn appropriate `@HD-SO` sort order header tag will be added or an existing one updated if necessary.\n\nNote that to generate an index file (by specifying `--output_bai`), the default coordinate sort must be used.\nThus the `--sort_by_read_names` and `--sort_by <TAG>` options are incompatible with `--output_bai`. \n'
   author = 'Robrecht Cannoodt, Angela Oliveira Pisco'
 }
diff --git a/target/nextflow/mapping/star_align/.config.vsh.yaml b/target/nextflow/mapping/star_align/.config.vsh.yaml
index 4e1278d9..a568592a 100644
--- a/target/nextflow/mapping/star_align/.config.vsh.yaml
+++ b/target/nextflow/mapping/star_align/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "star_align"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -2341,7 +2341,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -2371,11 +2371,11 @@ build_info:
   output: "target/nextflow/mapping/star_align"
   executable: "target/nextflow/mapping/star_align/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -2405,7 +2405,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/star_align/main.nf b/target/nextflow/mapping/star_align/main.nf
index f073ab18..18a7afcb 100644
--- a/target/nextflow/mapping/star_align/main.nf
+++ b/target/nextflow/mapping/star_align/main.nf
@@ -1,4 +1,4 @@
-// star_align v4.0.0
+// star_align v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "star_align",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -5466,7 +5466,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -5502,12 +5502,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/star_align",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -5532,7 +5532,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -6340,7 +6340,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/star_align",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/star_align/nextflow.config b/target/nextflow/mapping/star_align/nextflow.config
index 4e0fff72..bf0870f5 100644
--- a/target/nextflow/mapping/star_align/nextflow.config
+++ b/target/nextflow/mapping/star_align/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/star_align'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Align fastq files using STAR.'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml
index fe4a6675..4cd8fd57 100644
--- a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml
+++ b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "star_align_v273a"
 namespace: "mapping"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -2341,7 +2341,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -2371,11 +2371,11 @@ build_info:
   output: "target/nextflow/mapping/star_align_v273a"
   executable: "target/nextflow/mapping/star_align_v273a/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -2405,7 +2405,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/mapping/star_align_v273a/main.nf b/target/nextflow/mapping/star_align_v273a/main.nf
index a0abb7c7..95e497b6 100644
--- a/target/nextflow/mapping/star_align_v273a/main.nf
+++ b/target/nextflow/mapping/star_align_v273a/main.nf
@@ -1,4 +1,4 @@
-// star_align_v273a v4.0.0
+// star_align_v273a v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "star_align_v273a",
   "namespace" : "mapping",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -5466,7 +5466,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -5502,12 +5502,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/mapping/star_align_v273a",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -5532,7 +5532,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -6340,7 +6340,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/mapping/star_align_v273a",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/mapping/star_align_v273a/nextflow.config b/target/nextflow/mapping/star_align_v273a/nextflow.config
index b07331c0..1ca0246c 100644
--- a/target/nextflow/mapping/star_align_v273a/nextflow.config
+++ b/target/nextflow/mapping/star_align_v273a/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'mapping/star_align_v273a'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Align fastq files using STAR.'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/metadata/add_id/.config.vsh.yaml b/target/nextflow/metadata/add_id/.config.vsh.yaml
index 5de843ac..64ad0207 100644
--- a/target/nextflow/metadata/add_id/.config.vsh.yaml
+++ b/target/nextflow/metadata/add_id/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "add_id"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -185,7 +185,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -226,11 +226,11 @@ build_info:
   output: "target/nextflow/metadata/add_id"
   executable: "target/nextflow/metadata/add_id/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -260,7 +260,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/metadata/add_id/main.nf b/target/nextflow/metadata/add_id/main.nf
index 37499a0b..f994ca25 100644
--- a/target/nextflow/metadata/add_id/main.nf
+++ b/target/nextflow/metadata/add_id/main.nf
@@ -1,4 +1,4 @@
-// add_id v4.0.0
+// add_id v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "add_id",
   "namespace" : "metadata",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3269,7 +3269,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3325,12 +3325,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/metadata/add_id",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3355,7 +3355,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3871,7 +3871,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/metadata/add_id",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/metadata/add_id/nextflow.config b/target/nextflow/metadata/add_id/nextflow.config
index 01e0efbc..856076a4 100644
--- a/target/nextflow/metadata/add_id/nextflow.config
+++ b/target/nextflow/metadata/add_id/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'metadata/add_id'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Add id of .obs. Also allows to make .obs_names (the .obs index) unique \nby prefixing the values with an unique id per .h5mu file.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml
index 9ab246af..dc167c40 100644
--- a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml
+++ b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "grep_annotation_column"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -241,7 +241,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -282,11 +282,11 @@ build_info:
   output: "target/nextflow/metadata/grep_annotation_column"
   executable: "target/nextflow/metadata/grep_annotation_column/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -316,7 +316,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/metadata/grep_annotation_column/main.nf b/target/nextflow/metadata/grep_annotation_column/main.nf
index 665edca3..c0692094 100644
--- a/target/nextflow/metadata/grep_annotation_column/main.nf
+++ b/target/nextflow/metadata/grep_annotation_column/main.nf
@@ -1,4 +1,4 @@
-// grep_annotation_column v4.0.0
+// grep_annotation_column v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "grep_annotation_column",
   "namespace" : "metadata",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3335,7 +3335,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3391,12 +3391,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/metadata/grep_annotation_column",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3421,7 +3421,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4010,7 +4010,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/metadata/grep_annotation_column",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/metadata/grep_annotation_column/nextflow.config b/target/nextflow/metadata/grep_annotation_column/nextflow.config
index 5d333acd..1d30120f 100644
--- a/target/nextflow/metadata/grep_annotation_column/nextflow.config
+++ b/target/nextflow/metadata/grep_annotation_column/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'metadata/grep_annotation_column'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Perform a regex lookup on a column from the annotation matrices .obs or .var.\nThe annotation matrix can originate from either a modality, or all modalities (global .var or .obs).\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/metadata/join_csv/.config.vsh.yaml b/target/nextflow/metadata/join_csv/.config.vsh.yaml
index c3125742..f060e75b 100644
--- a/target/nextflow/metadata/join_csv/.config.vsh.yaml
+++ b/target/nextflow/metadata/join_csv/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "join_csv"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -216,7 +216,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -257,11 +257,11 @@ build_info:
   output: "target/nextflow/metadata/join_csv"
   executable: "target/nextflow/metadata/join_csv/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -291,7 +291,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/metadata/join_csv/main.nf b/target/nextflow/metadata/join_csv/main.nf
index 1c92368b..20f153ec 100644
--- a/target/nextflow/metadata/join_csv/main.nf
+++ b/target/nextflow/metadata/join_csv/main.nf
@@ -1,4 +1,4 @@
-// join_csv v4.0.0
+// join_csv v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "join_csv",
   "namespace" : "metadata",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3308,7 +3308,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3364,12 +3364,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/metadata/join_csv",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3394,7 +3394,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3887,7 +3887,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/metadata/join_csv",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/metadata/join_csv/nextflow.config b/target/nextflow/metadata/join_csv/nextflow.config
index 866be826..a15f33cc 100644
--- a/target/nextflow/metadata/join_csv/nextflow.config
+++ b/target/nextflow/metadata/join_csv/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'metadata/join_csv'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Join a csv containing metadata to the .obs or .var field of a mudata file.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml
index 2f293f97..00ad736f 100644
--- a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml
+++ b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "join_uns_to_obs"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -164,7 +164,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -205,11 +205,11 @@ build_info:
   output: "target/nextflow/metadata/join_uns_to_obs"
   executable: "target/nextflow/metadata/join_uns_to_obs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -239,7 +239,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/metadata/join_uns_to_obs/main.nf b/target/nextflow/metadata/join_uns_to_obs/main.nf
index 23101cd1..24591375 100644
--- a/target/nextflow/metadata/join_uns_to_obs/main.nf
+++ b/target/nextflow/metadata/join_uns_to_obs/main.nf
@@ -1,4 +1,4 @@
-// join_uns_to_obs v4.0.0
+// join_uns_to_obs v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "join_uns_to_obs",
   "namespace" : "metadata",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3236,7 +3236,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3292,12 +3292,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/metadata/join_uns_to_obs",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3322,7 +3322,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3799,7 +3799,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/metadata/join_uns_to_obs",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/metadata/join_uns_to_obs/nextflow.config b/target/nextflow/metadata/join_uns_to_obs/nextflow.config
index 76d07b88..7847e700 100644
--- a/target/nextflow/metadata/join_uns_to_obs/nextflow.config
+++ b/target/nextflow/metadata/join_uns_to_obs/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'metadata/join_uns_to_obs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Join a data frame of length 1 (1 row index value) in .uns containing metadata to the .obs of a mudata file.'
 }
 
diff --git a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml
index 10676ed7..9a303374 100644
--- a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml
+++ b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_obsm_to_obs"
 namespace: "metadata"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -183,7 +183,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -224,11 +224,11 @@ build_info:
   output: "target/nextflow/metadata/move_obsm_to_obs"
   executable: "target/nextflow/metadata/move_obsm_to_obs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -258,7 +258,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/metadata/move_obsm_to_obs/main.nf b/target/nextflow/metadata/move_obsm_to_obs/main.nf
index 2d61de86..c7d9e0be 100644
--- a/target/nextflow/metadata/move_obsm_to_obs/main.nf
+++ b/target/nextflow/metadata/move_obsm_to_obs/main.nf
@@ -1,4 +1,4 @@
-// move_obsm_to_obs v4.0.0
+// move_obsm_to_obs v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "move_obsm_to_obs",
   "namespace" : "metadata",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3268,7 +3268,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3324,12 +3324,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/metadata/move_obsm_to_obs",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3354,7 +3354,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3860,7 +3860,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/metadata/move_obsm_to_obs",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/metadata/move_obsm_to_obs/nextflow.config b/target/nextflow/metadata/move_obsm_to_obs/nextflow.config
index f76bc547..8d639c2c 100644
--- a/target/nextflow/metadata/move_obsm_to_obs/nextflow.config
+++ b/target/nextflow/metadata/move_obsm_to_obs/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'metadata/move_obsm_to_obs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Move a matrix from .obsm to .obs. Newly created columns in .obs will \nbe created from the .obsm key suffixed with an underscore and the name of the columns\nof the specified .obsm matrix.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/neighbors/bbknn/.config.vsh.yaml b/target/nextflow/neighbors/bbknn/.config.vsh.yaml
index 5b792ff2..97a840cd 100644
--- a/target/nextflow/neighbors/bbknn/.config.vsh.yaml
+++ b/target/nextflow/neighbors/bbknn/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bbknn"
 namespace: "neighbors"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -272,7 +272,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -310,11 +310,11 @@ build_info:
   output: "target/nextflow/neighbors/bbknn"
   executable: "target/nextflow/neighbors/bbknn/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -344,7 +344,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/neighbors/bbknn/main.nf b/target/nextflow/neighbors/bbknn/main.nf
index 6e9e1afb..72452250 100644
--- a/target/nextflow/neighbors/bbknn/main.nf
+++ b/target/nextflow/neighbors/bbknn/main.nf
@@ -1,4 +1,4 @@
-// bbknn v4.0.0
+// bbknn v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bbknn",
   "namespace" : "neighbors",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3367,7 +3367,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3416,12 +3416,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/neighbors/bbknn",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3446,7 +3446,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3929,7 +3929,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/neighbors/bbknn",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/neighbors/bbknn/nextflow.config b/target/nextflow/neighbors/bbknn/nextflow.config
index 5f0d419f..8b856ddf 100644
--- a/target/nextflow/neighbors/bbknn/nextflow.config
+++ b/target/nextflow/neighbors/bbknn/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'neighbors/bbknn'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'BBKNN network generation\n'
   author = 'Dries De Maeyer, Dries Schaumont'
 }
diff --git a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml
index 4ca02d74..155b39cf 100644
--- a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml
+++ b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "find_neighbors"
 namespace: "neighbors"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -296,7 +296,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -338,11 +338,11 @@ build_info:
   output: "target/nextflow/neighbors/find_neighbors"
   executable: "target/nextflow/neighbors/find_neighbors/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -372,7 +372,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/neighbors/find_neighbors/main.nf b/target/nextflow/neighbors/find_neighbors/main.nf
index a0748335..4f4d0bf8 100644
--- a/target/nextflow/neighbors/find_neighbors/main.nf
+++ b/target/nextflow/neighbors/find_neighbors/main.nf
@@ -1,4 +1,4 @@
-// find_neighbors v4.0.0
+// find_neighbors v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "find_neighbors",
   "namespace" : "neighbors",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3395,7 +3395,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3452,12 +3452,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/neighbors/find_neighbors",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3482,7 +3482,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3983,7 +3983,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/neighbors/find_neighbors",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/neighbors/find_neighbors/nextflow.config b/target/nextflow/neighbors/find_neighbors/nextflow.config
index c79a63e6..4cf6f559 100644
--- a/target/nextflow/neighbors/find_neighbors/nextflow.config
+++ b/target/nextflow/neighbors/find_neighbors/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'neighbors/find_neighbors'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Compute a neighborhood graph of observations [McInnes18].\n\nThe neighbor search efficiency of this heavily relies on UMAP [McInnes18], which also provides a method for estimating connectivities of data points - the connectivity of the manifold (method==\'umap\'). If method==\'gauss\', connectivities are computed according to [Coifman05], in the adaption of [Haghverdi16].\n'
   author = 'Dries De Maeyer, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml
index 833e5ca1..5a1c2c88 100644
--- a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml
+++ b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "filter_10xh5"
 namespace: "process_10xh5"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -182,7 +182,7 @@ engines:
   id: "docker"
   image: "eddelbuettel/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -226,11 +226,11 @@ build_info:
   output: "target/nextflow/process_10xh5/filter_10xh5"
   executable: "target/nextflow/process_10xh5/filter_10xh5/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -260,7 +260,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/process_10xh5/filter_10xh5/main.nf b/target/nextflow/process_10xh5/filter_10xh5/main.nf
index 60fac7b1..1a02cf2d 100644
--- a/target/nextflow/process_10xh5/filter_10xh5/main.nf
+++ b/target/nextflow/process_10xh5/filter_10xh5/main.nf
@@ -1,4 +1,4 @@
-// filter_10xh5 v4.0.0
+// filter_10xh5 v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "filter_10xh5",
   "namespace" : "process_10xh5",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3264,7 +3264,7 @@ meta = [
       "id" : "docker",
       "image" : "eddelbuettel/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3321,12 +3321,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/process_10xh5/filter_10xh5",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3351,7 +3351,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3886,7 +3886,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/process_10xh5/filter_10xh5",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/process_10xh5/filter_10xh5/nextflow.config b/target/nextflow/process_10xh5/filter_10xh5/nextflow.config
index 6a9c9caa..f071be72 100644
--- a/target/nextflow/process_10xh5/filter_10xh5/nextflow.config
+++ b/target/nextflow/process_10xh5/filter_10xh5/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'process_10xh5/filter_10xh5'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Filter a 10x h5 dataset.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml b/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml
index 5c39c0a3..bd5000c8 100644
--- a/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml
+++ b/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "calculate_atac_qc_metrics"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -249,7 +249,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -283,11 +283,11 @@ build_info:
   output: "target/nextflow/qc/calculate_atac_qc_metrics"
   executable: "target/nextflow/qc/calculate_atac_qc_metrics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -317,7 +317,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/qc/calculate_atac_qc_metrics/main.nf b/target/nextflow/qc/calculate_atac_qc_metrics/main.nf
index 8ec14ef3..b5a4581c 100644
--- a/target/nextflow/qc/calculate_atac_qc_metrics/main.nf
+++ b/target/nextflow/qc/calculate_atac_qc_metrics/main.nf
@@ -1,4 +1,4 @@
-// calculate_atac_qc_metrics v4.0.0
+// calculate_atac_qc_metrics v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "calculate_atac_qc_metrics",
   "namespace" : "qc",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3331,7 +3331,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3377,12 +3377,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/qc/calculate_atac_qc_metrics",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3407,7 +3407,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3946,7 +3946,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/qc/calculate_atac_qc_metrics",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config b/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config
index 5aad8a03..95e0385c 100644
--- a/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config
+++ b/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'qc/calculate_atac_qc_metrics'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Add basic ATAC quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nObs metrics (name in this component -> name in scanpy):\n  - n_features_per_cell -> n_genes_by_counts\n  - total_fragment_counts -> total_counts\n    \n'
   author = 'Vladimir Shitov'
 }
diff --git a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml
index 16565466..00fd9e51 100644
--- a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml
+++ b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "calculate_qc_metrics"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -295,7 +295,7 @@ engines:
   id: "docker"
   image: "python:3.11-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -342,11 +342,11 @@ build_info:
   output: "target/nextflow/qc/calculate_qc_metrics"
   executable: "target/nextflow/qc/calculate_qc_metrics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -376,7 +376,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/qc/calculate_qc_metrics/main.nf b/target/nextflow/qc/calculate_qc_metrics/main.nf
index d5e80753..b532a6db 100644
--- a/target/nextflow/qc/calculate_qc_metrics/main.nf
+++ b/target/nextflow/qc/calculate_qc_metrics/main.nf
@@ -1,4 +1,4 @@
-// calculate_qc_metrics v4.0.0
+// calculate_qc_metrics v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "calculate_qc_metrics",
   "namespace" : "qc",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3381,7 +3381,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3446,12 +3446,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/qc/calculate_qc_metrics",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3476,7 +3476,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4107,7 +4107,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/qc/calculate_qc_metrics",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/qc/calculate_qc_metrics/nextflow.config b/target/nextflow/qc/calculate_qc_metrics/nextflow.config
index e0022410..3f5d4e0d 100644
--- a/target/nextflow/qc/calculate_qc_metrics/nextflow.config
+++ b/target/nextflow/qc/calculate_qc_metrics/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'qc/calculate_qc_metrics'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Add basic quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nVar metrics (name in this component -> name in scanpy):\n  - pct_dropout -> pct_dropout_by_{expr_type}\n  - num_nonzero_obs -> n_cells_by_{expr_type}\n  - obs_mean -> mean_{expr_type}\n  - total_counts -> total_{expr_type}\n\n  Obs metrics:\n    - num_nonzero_vars -> n_genes_by_{expr_type}\n    - pct_{var_qc_metrics} -> pct_{expr_type}_{qc_var}\n    - total_counts_{var_qc_metrics} -> total_{expr_type}_{qc_var}\n    - pct_of_counts_in_top_{top_n_vars}_vars -> pct_{expr_type}_in_top_{n}_{var_type}\n    - total_counts -> total_{expr_type}\n    \n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/qc/fastqc/.config.vsh.yaml b/target/nextflow/qc/fastqc/.config.vsh.yaml
index b999e9b6..550a1dfd 100644
--- a/target/nextflow/qc/fastqc/.config.vsh.yaml
+++ b/target/nextflow/qc/fastqc/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "fastqc"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -158,7 +158,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -176,11 +176,11 @@ build_info:
   output: "target/nextflow/qc/fastqc"
   executable: "target/nextflow/qc/fastqc/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -210,7 +210,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/qc/fastqc/main.nf b/target/nextflow/qc/fastqc/main.nf
index a2c79d68..b3675c03 100644
--- a/target/nextflow/qc/fastqc/main.nf
+++ b/target/nextflow/qc/fastqc/main.nf
@@ -1,4 +1,4 @@
-// fastqc v4.0.0
+// fastqc v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "fastqc",
   "namespace" : "qc",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3226,7 +3226,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3249,12 +3249,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/qc/fastqc",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3279,7 +3279,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3726,7 +3726,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/qc/fastqc",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowcpu",
diff --git a/target/nextflow/qc/fastqc/nextflow.config b/target/nextflow/qc/fastqc/nextflow.config
index aa215b49..142c7c9f 100644
--- a/target/nextflow/qc/fastqc/nextflow.config
+++ b/target/nextflow/qc/fastqc/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'qc/fastqc'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can take one or more files (by means of shell globbing) or a complete directory.\n'
 }
 
diff --git a/target/nextflow/qc/multiqc/.config.vsh.yaml b/target/nextflow/qc/multiqc/.config.vsh.yaml
index 8e819fa5..39b3ce94 100644
--- a/target/nextflow/qc/multiqc/.config.vsh.yaml
+++ b/target/nextflow/qc/multiqc/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "multiqc"
 namespace: "qc"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -133,7 +133,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -162,11 +162,11 @@ build_info:
   output: "target/nextflow/qc/multiqc"
   executable: "target/nextflow/qc/multiqc/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -196,7 +196,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/qc/multiqc/main.nf b/target/nextflow/qc/multiqc/main.nf
index 7f96f800..ec4eb47b 100644
--- a/target/nextflow/qc/multiqc/main.nf
+++ b/target/nextflow/qc/multiqc/main.nf
@@ -1,4 +1,4 @@
-// multiqc v4.0.0
+// multiqc v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "multiqc",
   "namespace" : "qc",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3195,7 +3195,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3236,12 +3236,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/qc/multiqc",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3266,7 +3266,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3712,7 +3712,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/qc/multiqc",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/qc/multiqc/nextflow.config b/target/nextflow/qc/multiqc/nextflow.config
index b7370ae3..62a364dd 100644
--- a/target/nextflow/qc/multiqc/nextflow.config
+++ b/target/nextflow/qc/multiqc/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'qc/multiqc'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n'
 }
 
diff --git a/target/nextflow/query/cellxgene_census/.config.vsh.yaml b/target/nextflow/query/cellxgene_census/.config.vsh.yaml
index a9a310dc..af8b6520 100644
--- a/target/nextflow/query/cellxgene_census/.config.vsh.yaml
+++ b/target/nextflow/query/cellxgene_census/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellxgene_census"
 namespace: "query"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Matthias Beyens"
   roles:
@@ -506,7 +506,7 @@ engines:
   id: "docker"
   image: "python:3.11"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -539,11 +539,11 @@ build_info:
   output: "target/nextflow/query/cellxgene_census"
   executable: "target/nextflow/query/cellxgene_census/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -573,7 +573,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/query/cellxgene_census/main.nf b/target/nextflow/query/cellxgene_census/main.nf
index 7198b2af..26348b5f 100644
--- a/target/nextflow/query/cellxgene_census/main.nf
+++ b/target/nextflow/query/cellxgene_census/main.nf
@@ -1,4 +1,4 @@
-// cellxgene_census v4.0.0
+// cellxgene_census v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3038,7 +3038,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellxgene_census",
   "namespace" : "query",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Matthias Beyens",
@@ -3653,7 +3653,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.11",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3694,12 +3694,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/query/cellxgene_census",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3724,7 +3724,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4355,7 +4355,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/query/cellxgene_census",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/query/cellxgene_census/nextflow.config b/target/nextflow/query/cellxgene_census/nextflow.config
index 3614ed68..6972d71e 100644
--- a/target/nextflow/query/cellxgene_census/nextflow.config
+++ b/target/nextflow/query/cellxgene_census/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'query/cellxgene_census'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Query cells from a CellxGene Census or custom TileDBSoma object.\nAside from fetching the cells\' RNA counts (`.X`), cell metadata\n(`.obs`) and gene metadata (`.var`), this component also fetches\nthe dataset metadata and joins it into the cell metadata.\n'
   author = 'Matthias Beyens, Dries De Maeyer, Robrecht Cannoodt, Kai Waldrant'
 }
diff --git a/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml b/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml
index 24e9dcd7..b6413616 100644
--- a/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml
+++ b/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tiledb_healthcheck"
 namespace: "query"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -137,7 +137,7 @@ engines:
   id: "docker"
   image: "python:3.12"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "python"
@@ -162,11 +162,11 @@ build_info:
   output: "target/nextflow/query/tiledb_healthcheck"
   executable: "target/nextflow/query/tiledb_healthcheck/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -196,7 +196,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/query/tiledb_healthcheck/main.nf b/target/nextflow/query/tiledb_healthcheck/main.nf
index 2eb02b26..928c5ec9 100644
--- a/target/nextflow/query/tiledb_healthcheck/main.nf
+++ b/target/nextflow/query/tiledb_healthcheck/main.nf
@@ -1,4 +1,4 @@
-// tiledb_healthcheck v4.0.0
+// tiledb_healthcheck v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "tiledb_healthcheck",
   "namespace" : "query",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3211,7 +3211,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3245,12 +3245,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/query/tiledb_healthcheck",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3275,7 +3275,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3744,7 +3744,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/query/tiledb_healthcheck",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/query/tiledb_healthcheck/nextflow.config b/target/nextflow/query/tiledb_healthcheck/nextflow.config
index ee466c85..acc81269 100644
--- a/target/nextflow/query/tiledb_healthcheck/nextflow.config
+++ b/target/nextflow/query/tiledb_healthcheck/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'query/tiledb_healthcheck'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Checks if a provided location can be queried as a TileDB-SOMA database.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml
index 3a9d4ea5..23da64e6 100644
--- a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml
+++ b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_bdrhap_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -249,7 +249,7 @@ engines:
   id: "docker"
   image: "bdgenomics/rhapsody:2.2.1"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -274,11 +274,11 @@ build_info:
   output: "target/nextflow/reference/build_bdrhap_reference"
   executable: "target/nextflow/reference/build_bdrhap_reference/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -308,7 +308,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/reference/build_bdrhap_reference/main.nf b/target/nextflow/reference/build_bdrhap_reference/main.nf
index 553d4e85..df1e9767 100644
--- a/target/nextflow/reference/build_bdrhap_reference/main.nf
+++ b/target/nextflow/reference/build_bdrhap_reference/main.nf
@@ -1,4 +1,4 @@
-// build_bdrhap_reference v4.0.0
+// build_bdrhap_reference v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "build_bdrhap_reference",
   "namespace" : "reference",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3341,7 +3341,7 @@ meta = [
       "id" : "docker",
       "image" : "bdgenomics/rhapsody:2.2.1",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3374,12 +3374,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/reference/build_bdrhap_reference",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3404,7 +3404,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4009,7 +4009,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/reference/build_bdrhap_reference",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/reference/build_bdrhap_reference/nextflow.config b/target/nextflow/reference/build_bdrhap_reference/nextflow.config
index 7d8d0f2e..3a6b4b6d 100644
--- a/target/nextflow/reference/build_bdrhap_reference/nextflow.config
+++ b/target/nextflow/reference/build_bdrhap_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'reference/build_bdrhap_reference'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'The Reference Files Generator creates an archive containing Genome Index\nand Transcriptome annotation files needed for the BD Rhapsody Sequencing\nAnalysis Pipeline. The app takes as input one or more FASTA and GTF files\nand produces a compressed archive in the form of a tar.gz file. The \narchive contains:\n  \n- STAR index\n- Filtered GTF file\n'
   author = 'Robrecht Cannoodt, Weiwei Schultz'
 }
diff --git a/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml b/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml
index 54fee89d..2a15bddb 100644
--- a/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml
+++ b/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_cellranger_arc_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -213,7 +213,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger_arc:2.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -246,11 +246,11 @@ build_info:
   output: "target/nextflow/reference/build_cellranger_arc_reference"
   executable: "target/nextflow/reference/build_cellranger_arc_reference/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/reference/build_cellranger_arc_reference/main.nf b/target/nextflow/reference/build_cellranger_arc_reference/main.nf
index 4dfc3f41..a78c6158 100644
--- a/target/nextflow/reference/build_cellranger_arc_reference/main.nf
+++ b/target/nextflow/reference/build_cellranger_arc_reference/main.nf
@@ -1,4 +1,4 @@
-// build_cellranger_arc_reference v4.0.0
+// build_cellranger_arc_reference v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "build_cellranger_arc_reference",
   "namespace" : "reference",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3295,7 +3295,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/cellranger_arc:2.0",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3336,12 +3336,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/reference/build_cellranger_arc_reference",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3366,7 +3366,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3875,7 +3875,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/reference/build_cellranger_arc_reference",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config b/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config
index 148a8c4b..d4eb1d9d 100644
--- a/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config
+++ b/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'reference/build_cellranger_arc_reference'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Build a Cell Ranger-arc and -atac compatible reference folder from user-supplied genome FASTA and gene GTF files. Creates a new folder named after the genome.'
   author = 'Vladimir Shitov'
 }
diff --git a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml
index ffdd28f6..3f48d2be 100644
--- a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml
+++ b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_cellranger_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -182,7 +182,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -214,11 +214,11 @@ build_info:
   output: "target/nextflow/reference/build_cellranger_reference"
   executable: "target/nextflow/reference/build_cellranger_reference/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/reference/build_cellranger_reference/main.nf b/target/nextflow/reference/build_cellranger_reference/main.nf
index 7cb8f998..36c75b66 100644
--- a/target/nextflow/reference/build_cellranger_reference/main.nf
+++ b/target/nextflow/reference/build_cellranger_reference/main.nf
@@ -1,4 +1,4 @@
-// build_cellranger_reference v4.0.0
+// build_cellranger_reference v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "build_cellranger_reference",
   "namespace" : "reference",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3272,7 +3272,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/cellranger:9.0",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3310,12 +3310,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/reference/build_cellranger_reference",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3340,7 +3340,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3809,7 +3809,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/reference/build_cellranger_reference",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/reference/build_cellranger_reference/nextflow.config b/target/nextflow/reference/build_cellranger_reference/nextflow.config
index b89dee07..564e60ef 100644
--- a/target/nextflow/reference/build_cellranger_reference/nextflow.config
+++ b/target/nextflow/reference/build_cellranger_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'reference/build_cellranger_reference'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files. Creates a new folder named after the genome.'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/reference/build_star_reference/.config.vsh.yaml b/target/nextflow/reference/build_star_reference/.config.vsh.yaml
index 01962910..cb51e45c 100644
--- a/target/nextflow/reference/build_star_reference/.config.vsh.yaml
+++ b/target/nextflow/reference/build_star_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "build_star_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -208,11 +208,11 @@ build_info:
   output: "target/nextflow/reference/build_star_reference"
   executable: "target/nextflow/reference/build_star_reference/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -242,7 +242,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/reference/build_star_reference/main.nf b/target/nextflow/reference/build_star_reference/main.nf
index 5775bf48..2a837614 100644
--- a/target/nextflow/reference/build_star_reference/main.nf
+++ b/target/nextflow/reference/build_star_reference/main.nf
@@ -1,4 +1,4 @@
-// build_star_reference v4.0.0
+// build_star_reference v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "build_star_reference",
   "namespace" : "reference",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3254,7 +3254,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3290,12 +3290,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/reference/build_star_reference",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3320,7 +3320,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3907,7 +3907,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/reference/build_star_reference",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/reference/build_star_reference/nextflow.config b/target/nextflow/reference/build_star_reference/nextflow.config
index f515d644..e468af93 100644
--- a/target/nextflow/reference/build_star_reference/nextflow.config
+++ b/target/nextflow/reference/build_star_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'reference/build_star_reference'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Create a reference for STAR from a set of fasta files.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml b/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml
index 2032857a..8fbffb17 100644
--- a/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml
+++ b/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_mkgtf"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -152,7 +152,7 @@ engines:
   id: "docker"
   image: "ghcr.io/data-intuitive/cellranger:9.0"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -182,11 +182,11 @@ build_info:
   output: "target/nextflow/reference/cellranger_mkgtf"
   executable: "target/nextflow/reference/cellranger_mkgtf/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -216,7 +216,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/reference/cellranger_mkgtf/main.nf b/target/nextflow/reference/cellranger_mkgtf/main.nf
index 68398e74..b46a7a8e 100644
--- a/target/nextflow/reference/cellranger_mkgtf/main.nf
+++ b/target/nextflow/reference/cellranger_mkgtf/main.nf
@@ -1,4 +1,4 @@
-// cellranger_mkgtf v4.0.0
+// cellranger_mkgtf v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_mkgtf",
   "namespace" : "reference",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3228,7 +3228,7 @@ meta = [
       "id" : "docker",
       "image" : "ghcr.io/data-intuitive/cellranger:9.0",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3270,12 +3270,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/reference/cellranger_mkgtf",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3300,7 +3300,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3773,7 +3773,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/reference/cellranger_mkgtf",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/reference/cellranger_mkgtf/nextflow.config b/target/nextflow/reference/cellranger_mkgtf/nextflow.config
index 38cf5a4b..78275b6c 100644
--- a/target/nextflow/reference/cellranger_mkgtf/nextflow.config
+++ b/target/nextflow/reference/cellranger_mkgtf/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'reference/cellranger_mkgtf'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Make a GTF file - filter by a specific attribute.'
   author = 'Jakub Majercik'
 }
diff --git a/target/nextflow/reference/make_reference/.config.vsh.yaml b/target/nextflow/reference/make_reference/.config.vsh.yaml
index 408f1eb9..bd8d02b6 100644
--- a/target/nextflow/reference/make_reference/.config.vsh.yaml
+++ b/target/nextflow/reference/make_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "make_reference"
 namespace: "reference"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -208,7 +208,7 @@ engines:
   id: "docker"
   image: "ubuntu:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -231,11 +231,11 @@ build_info:
   output: "target/nextflow/reference/make_reference"
   executable: "target/nextflow/reference/make_reference/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -265,7 +265,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/reference/make_reference/main.nf b/target/nextflow/reference/make_reference/main.nf
index 0e28e404..a391e9a9 100644
--- a/target/nextflow/reference/make_reference/main.nf
+++ b/target/nextflow/reference/make_reference/main.nf
@@ -1,4 +1,4 @@
-// make_reference v4.0.0
+// make_reference v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "make_reference",
   "namespace" : "reference",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3299,7 +3299,7 @@ meta = [
       "id" : "docker",
       "image" : "ubuntu:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3327,12 +3327,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/reference/make_reference",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3357,7 +3357,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3862,7 +3862,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/reference/make_reference",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/reference/make_reference/nextflow.config b/target/nextflow/reference/make_reference/nextflow.config
index 9ad0ca0d..fb432a6a 100644
--- a/target/nextflow/reference/make_reference/nextflow.config
+++ b/target/nextflow/reference/make_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'reference/make_reference'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Preprocess and build a transcriptome reference.\n\nExample input files are:\n  - `genome_fasta`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz\n  - `transcriptome_gtf`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz\n  - `ercc`: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\n'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/report/mermaid/.config.vsh.yaml b/target/nextflow/report/mermaid/.config.vsh.yaml
index 424eddca..b6f5925f 100644
--- a/target/nextflow/report/mermaid/.config.vsh.yaml
+++ b/target/nextflow/report/mermaid/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "mermaid"
 namespace: "report"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -182,7 +182,7 @@ engines:
   id: "docker"
   image: "node:20-bullseye"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "javascript"
@@ -203,11 +203,11 @@ build_info:
   output: "target/nextflow/report/mermaid"
   executable: "target/nextflow/report/mermaid/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -237,7 +237,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/report/mermaid/main.nf b/target/nextflow/report/mermaid/main.nf
index 6c5478a1..007f9ce7 100644
--- a/target/nextflow/report/mermaid/main.nf
+++ b/target/nextflow/report/mermaid/main.nf
@@ -1,4 +1,4 @@
-// mermaid v4.0.0
+// mermaid v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "mermaid",
   "namespace" : "report",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3264,7 +3264,7 @@ meta = [
       "id" : "docker",
       "image" : "node:20-bullseye",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3293,12 +3293,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/report/mermaid",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3323,7 +3323,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3770,7 +3770,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/report/mermaid",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "tag" : "$id"
 }'''),
diff --git a/target/nextflow/report/mermaid/nextflow.config b/target/nextflow/report/mermaid/nextflow.config
index 2c18223f..3e2b9a78 100644
--- a/target/nextflow/report/mermaid/nextflow.config
+++ b/target/nextflow/report/mermaid/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'report/mermaid'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Generates a network from mermaid code.\n'
   author = 'Dries De Maeyer'
 }
diff --git a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml
index 5d5a737f..8e22ac21 100644
--- a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml
+++ b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "assert_test_workflow_2_output"
 namespace: "test_workflows/multiomics/process_samples"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   info:
@@ -136,7 +136,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -169,11 +169,11 @@ build_info:
   output: "target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output"
   executable: "target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -203,7 +203,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf
index 4d9732e7..553f8ad9 100644
--- a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf
+++ b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf
@@ -1,4 +1,4 @@
-// assert_test_workflow_2_output v4.0.0
+// assert_test_workflow_2_output v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "assert_test_workflow_2_output",
   "namespace" : "test_workflows/multiomics/process_samples",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3208,7 +3208,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3249,12 +3249,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3279,7 +3279,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3974,7 +3974,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/test_workflows/multiomics/process_samples/assert_test_workflow_2_output",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem"
diff --git a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config
index de567d1f..09b6dea3 100644
--- a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config
+++ b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'test_workflows/multiomics/process_samples/assert_test_workflow_2_output'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This component tests the output of the integration test of process_samples test_wf.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml b/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml
index 4282d39e..2b998860 100644
--- a/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml
+++ b/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bpcells_regress_out"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -224,7 +224,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -284,11 +284,11 @@ build_info:
   output: "target/nextflow/transform/bpcells_regress_out"
   executable: "target/nextflow/transform/bpcells_regress_out/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -318,7 +318,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/bpcells_regress_out/main.nf b/target/nextflow/transform/bpcells_regress_out/main.nf
index 6b0bdd88..c200f54c 100644
--- a/target/nextflow/transform/bpcells_regress_out/main.nf
+++ b/target/nextflow/transform/bpcells_regress_out/main.nf
@@ -1,4 +1,4 @@
-// bpcells_regress_out v4.0.0
+// bpcells_regress_out v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bpcells_regress_out",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3325,7 +3325,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3408,12 +3408,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/bpcells_regress_out",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3438,7 +3438,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3949,7 +3949,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/bpcells_regress_out",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/transform/bpcells_regress_out/nextflow.config b/target/nextflow/transform/bpcells_regress_out/nextflow.config
index be9750d2..b714ced4 100644
--- a/target/nextflow/transform/bpcells_regress_out/nextflow.config
+++ b/target/nextflow/transform/bpcells_regress_out/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/bpcells_regress_out'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Regress out the effects of confounding variables using a linear least squares regression model with BPCells.\n'
   author = 'Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz'
 }
diff --git a/target/nextflow/transform/clr/.config.vsh.yaml b/target/nextflow/transform/clr/.config.vsh.yaml
index cf57ba35..373d7513 100644
--- a/target/nextflow/transform/clr/.config.vsh.yaml
+++ b/target/nextflow/transform/clr/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "clr"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -203,7 +203,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -240,11 +240,11 @@ build_info:
   output: "target/nextflow/transform/clr"
   executable: "target/nextflow/transform/clr/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -274,7 +274,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/clr/main.nf b/target/nextflow/transform/clr/main.nf
index 59b623bd..58b7f6b0 100644
--- a/target/nextflow/transform/clr/main.nf
+++ b/target/nextflow/transform/clr/main.nf
@@ -1,4 +1,4 @@
-// clr v4.0.0
+// clr v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "clr",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3289,7 +3289,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3337,12 +3337,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/clr",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3367,7 +3367,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3853,7 +3853,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/clr",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/transform/clr/nextflow.config b/target/nextflow/transform/clr/nextflow.config
index 06b18230..0ba7413a 100644
--- a/target/nextflow/transform/clr/nextflow.config
+++ b/target/nextflow/transform/clr/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/clr'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017).\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/transform/delete_layer/.config.vsh.yaml b/target/nextflow/transform/delete_layer/.config.vsh.yaml
index c4417a55..3f4ef187 100644
--- a/target/nextflow/transform/delete_layer/.config.vsh.yaml
+++ b/target/nextflow/transform/delete_layer/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "delete_layer"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -186,7 +186,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -227,11 +227,11 @@ build_info:
   output: "target/nextflow/transform/delete_layer"
   executable: "target/nextflow/transform/delete_layer/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -261,7 +261,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/delete_layer/main.nf b/target/nextflow/transform/delete_layer/main.nf
index dad94094..cce03334 100644
--- a/target/nextflow/transform/delete_layer/main.nf
+++ b/target/nextflow/transform/delete_layer/main.nf
@@ -1,4 +1,4 @@
-// delete_layer v4.0.0
+// delete_layer v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "delete_layer",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3273,7 +3273,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3329,12 +3329,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/delete_layer",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3359,7 +3359,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3844,7 +3844,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/delete_layer",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/transform/delete_layer/nextflow.config b/target/nextflow/transform/delete_layer/nextflow.config
index ac515ab6..b935d697 100644
--- a/target/nextflow/transform/delete_layer/nextflow.config
+++ b/target/nextflow/transform/delete_layer/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/delete_layer'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Delete an anndata layer from one or more modalities.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/transform/log1p/.config.vsh.yaml b/target/nextflow/transform/log1p/.config.vsh.yaml
index 194c1d97..7bedc491 100644
--- a/target/nextflow/transform/log1p/.config.vsh.yaml
+++ b/target/nextflow/transform/log1p/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "log1p"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -217,7 +217,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -253,11 +253,11 @@ build_info:
   output: "target/nextflow/transform/log1p"
   executable: "target/nextflow/transform/log1p/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -287,7 +287,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/log1p/main.nf b/target/nextflow/transform/log1p/main.nf
index 17268a98..bb74f566 100644
--- a/target/nextflow/transform/log1p/main.nf
+++ b/target/nextflow/transform/log1p/main.nf
@@ -1,4 +1,4 @@
-// log1p v4.0.0
+// log1p v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "log1p",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3316,7 +3316,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3363,12 +3363,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/log1p",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3393,7 +3393,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3879,7 +3879,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/log1p",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/transform/log1p/nextflow.config b/target/nextflow/transform/log1p/nextflow.config
index d3c172a2..33620884 100644
--- a/target/nextflow/transform/log1p/nextflow.config
+++ b/target/nextflow/transform/log1p/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/log1p'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the natural logarithm unless a different base is given.\n'
   author = 'Dries De Maeyer, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/transform/move_layer/.config.vsh.yaml b/target/nextflow/transform/move_layer/.config.vsh.yaml
index b7f02d01..0215f2dc 100644
--- a/target/nextflow/transform/move_layer/.config.vsh.yaml
+++ b/target/nextflow/transform/move_layer/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "move_layer"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -176,7 +176,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -217,11 +217,11 @@ build_info:
   output: "target/nextflow/transform/move_layer"
   executable: "target/nextflow/transform/move_layer/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -251,7 +251,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/move_layer/main.nf b/target/nextflow/transform/move_layer/main.nf
index b01cdc9c..378702d8 100644
--- a/target/nextflow/transform/move_layer/main.nf
+++ b/target/nextflow/transform/move_layer/main.nf
@@ -1,4 +1,4 @@
-// move_layer v4.0.0
+// move_layer v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "move_layer",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3245,7 +3245,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3301,12 +3301,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/move_layer",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3331,7 +3331,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3818,7 +3818,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/move_layer",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "singlecpu",
diff --git a/target/nextflow/transform/move_layer/nextflow.config b/target/nextflow/transform/move_layer/nextflow.config
index f25a96d9..2d8f85bb 100644
--- a/target/nextflow/transform/move_layer/nextflow.config
+++ b/target/nextflow/transform/move_layer/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/move_layer'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Move a data matrix stored at the .layers or .X attributes in a MuData object to another layer.'
 }
 
diff --git a/target/nextflow/transform/normalize_total/.config.vsh.yaml b/target/nextflow/transform/normalize_total/.config.vsh.yaml
index eebbda28..61aa3c99 100644
--- a/target/nextflow/transform/normalize_total/.config.vsh.yaml
+++ b/target/nextflow/transform/normalize_total/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "normalize_total"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -229,7 +229,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -271,11 +271,11 @@ build_info:
   output: "target/nextflow/transform/normalize_total"
   executable: "target/nextflow/transform/normalize_total/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -305,7 +305,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/normalize_total/main.nf b/target/nextflow/transform/normalize_total/main.nf
index 100078f8..2c519bb2 100644
--- a/target/nextflow/transform/normalize_total/main.nf
+++ b/target/nextflow/transform/normalize_total/main.nf
@@ -1,4 +1,4 @@
-// normalize_total v4.0.0
+// normalize_total v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "normalize_total",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3319,7 +3319,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3376,12 +3376,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/normalize_total",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3406,7 +3406,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3896,7 +3896,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/normalize_total",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/transform/normalize_total/nextflow.config b/target/nextflow/transform/normalize_total/nextflow.config
index c2883370..b13f6a51 100644
--- a/target/nextflow/transform/normalize_total/nextflow.config
+++ b/target/nextflow/transform/normalize_total/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/normalize_total'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Normalize counts per cell.\n\nNormalize each cell by total counts over all genes, so that every cell has the same total count after normalization. If choosing target_sum=1e6, this is CPM normalization.\n\nIf exclude_highly_expressed=True, very highly expressed genes are excluded from the computation of the normalization factor (size factor) for each cell. This is meaningful as these can strongly influence the resulting normalized values for all other genes [Weinreb17].\n'
   author = 'Dries De Maeyer, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/transform/regress_out/.config.vsh.yaml b/target/nextflow/transform/regress_out/.config.vsh.yaml
index f3ec3d44..651f16ad 100644
--- a/target/nextflow/transform/regress_out/.config.vsh.yaml
+++ b/target/nextflow/transform/regress_out/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "regress_out"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -206,7 +206,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -248,11 +248,11 @@ build_info:
   output: "target/nextflow/transform/regress_out"
   executable: "target/nextflow/transform/regress_out/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -282,7 +282,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/regress_out/main.nf b/target/nextflow/transform/regress_out/main.nf
index 81da59fc..f57dfc16 100644
--- a/target/nextflow/transform/regress_out/main.nf
+++ b/target/nextflow/transform/regress_out/main.nf
@@ -1,4 +1,4 @@
-// regress_out v4.0.0
+// regress_out v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "regress_out",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3290,7 +3290,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3347,12 +3347,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/regress_out",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3377,7 +3377,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3861,7 +3861,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/regress_out",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/transform/regress_out/nextflow.config b/target/nextflow/transform/regress_out/nextflow.config
index 23c77776..4fd778e4 100644
--- a/target/nextflow/transform/regress_out/nextflow.config
+++ b/target/nextflow/transform/regress_out/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/regress_out'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Regress out (mostly) unwanted sources of variation.\nUses simple linear regression. This is inspired by Seurat\'s regressOut function in R [Satija15]. \nNote that this function tends to overcorrect in certain circumstances as described in issue theislab/scanpy#526.\nSee https://github.com/theislab/scanpy/issues/526.\n'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/transform/scale/.config.vsh.yaml b/target/nextflow/transform/scale/.config.vsh.yaml
index 11a004b7..72fcb896 100644
--- a/target/nextflow/transform/scale/.config.vsh.yaml
+++ b/target/nextflow/transform/scale/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scale"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -204,7 +204,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -246,11 +246,11 @@ build_info:
   output: "target/nextflow/transform/scale"
   executable: "target/nextflow/transform/scale/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/scale/main.nf b/target/nextflow/transform/scale/main.nf
index f3a1de82..50a741c5 100644
--- a/target/nextflow/transform/scale/main.nf
+++ b/target/nextflow/transform/scale/main.nf
@@ -1,4 +1,4 @@
-// scale v4.0.0
+// scale v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scale",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3291,7 +3291,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3348,12 +3348,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/scale",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3378,7 +3378,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3873,7 +3873,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/scale",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "lowmem",
diff --git a/target/nextflow/transform/scale/nextflow.config b/target/nextflow/transform/scale/nextflow.config
index 1a7adc02..b011135d 100644
--- a/target/nextflow/transform/scale/nextflow.config
+++ b/target/nextflow/transform/scale/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/scale'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Scale data to unit variance and zero mean.\n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/transform/tfidf/.config.vsh.yaml b/target/nextflow/transform/tfidf/.config.vsh.yaml
index f4cb1116..5178f4ab 100644
--- a/target/nextflow/transform/tfidf/.config.vsh.yaml
+++ b/target/nextflow/transform/tfidf/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "tfidf"
 namespace: "transform"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Vladimir Shitov"
   roles:
@@ -237,7 +237,7 @@ engines:
   id: "docker"
   image: "python:3.13-slim-bullseye"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -277,11 +277,11 @@ build_info:
   output: "target/nextflow/transform/tfidf"
   executable: "target/nextflow/transform/tfidf/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -311,7 +311,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/transform/tfidf/main.nf b/target/nextflow/transform/tfidf/main.nf
index ef800345..8c6873d3 100644
--- a/target/nextflow/transform/tfidf/main.nf
+++ b/target/nextflow/transform/tfidf/main.nf
@@ -1,4 +1,4 @@
-// tfidf v4.0.0
+// tfidf v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "tfidf",
   "namespace" : "transform",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Vladimir Shitov",
@@ -3325,7 +3325,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13-slim-bullseye",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3376,12 +3376,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/transform/tfidf",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3406,7 +3406,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3892,7 +3892,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/transform/tfidf",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "midmem",
diff --git a/target/nextflow/transform/tfidf/nextflow.config b/target/nextflow/transform/tfidf/nextflow.config
index bfececee..d35ffe42 100644
--- a/target/nextflow/transform/tfidf/nextflow.config
+++ b/target/nextflow/transform/tfidf/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'transform/tfidf'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Perform TF-IDF normalization of the data (typically, ATAC).\n\nTF-IDF stands for "term frequency - inverse document frequency". It is a technique from natural language processing analysis.\nIn the context of ATAC data, "terms" are the features (genes) and "documents" are the observations (cells). \nTF-IDF normalization is applied to single-cell ATAC-seq data to highlight the importance of specific genomic regions (typically peaks)\nacross different cells while down-weighting regions that are commonly accessible across many cells. \n'
   author = 'Vladimir Shitov'
 }
diff --git a/target/nextflow/velocity/scvelo/.config.vsh.yaml b/target/nextflow/velocity/scvelo/.config.vsh.yaml
index 07daed07..c0b98439 100644
--- a/target/nextflow/velocity/scvelo/.config.vsh.yaml
+++ b/target/nextflow/velocity/scvelo/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvelo"
 namespace: "velocity"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -311,7 +311,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -356,11 +356,11 @@ build_info:
   output: "target/nextflow/velocity/scvelo"
   executable: "target/nextflow/velocity/scvelo/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -390,7 +390,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/velocity/scvelo/main.nf b/target/nextflow/velocity/scvelo/main.nf
index d2ac832d..396e9a1a 100644
--- a/target/nextflow/velocity/scvelo/main.nf
+++ b/target/nextflow/velocity/scvelo/main.nf
@@ -1,4 +1,4 @@
-// scvelo v4.0.0
+// scvelo v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scvelo",
   "namespace" : "velocity",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3411,7 +3411,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3471,12 +3471,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/velocity/scvelo",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3501,7 +3501,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4111,7 +4111,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/velocity/scvelo",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/velocity/scvelo/nextflow.config b/target/nextflow/velocity/scvelo/nextflow.config
index d6813fbc..564338f8 100644
--- a/target/nextflow/velocity/scvelo/nextflow.config
+++ b/target/nextflow/velocity/scvelo/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'velocity/scvelo'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   author = 'Dries Schaumont'
 }
 
diff --git a/target/nextflow/velocity/velocyto/.config.vsh.yaml b/target/nextflow/velocity/velocyto/.config.vsh.yaml
index 670c2969..2ac81554 100644
--- a/target/nextflow/velocity/velocyto/.config.vsh.yaml
+++ b/target/nextflow/velocity/velocyto/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "velocyto"
 namespace: "velocity"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -202,7 +202,7 @@ engines:
   id: "docker"
   image: "python:3.13"
   target_registry: "images.viash-hub.com"
-  target_tag: "v4.0.0"
+  target_tag: "v4.0.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -246,11 +246,11 @@ build_info:
   output: "target/nextflow/velocity/velocyto"
   executable: "target/nextflow/velocity/velocyto/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -280,7 +280,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/velocity/velocyto/main.nf b/target/nextflow/velocity/velocyto/main.nf
index 0b9e69a8..4d34d6c3 100644
--- a/target/nextflow/velocity/velocyto/main.nf
+++ b/target/nextflow/velocity/velocyto/main.nf
@@ -1,4 +1,4 @@
-// velocyto v4.0.0
+// velocyto v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "velocyto",
   "namespace" : "velocity",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3292,7 +3292,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.13",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v4.0.0",
+      "target_tag" : "v4.0.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3355,12 +3355,12 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/velocity/velocyto",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3385,7 +3385,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3864,7 +3864,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/openpipeline/velocity/velocyto",
-    "tag" : "v4.0.0"
+    "tag" : "v4.0.1"
   },
   "label" : [
     "highmem",
diff --git a/target/nextflow/velocity/velocyto/nextflow.config b/target/nextflow/velocity/velocyto/nextflow.config
index c3d43391..96b19188 100644
--- a/target/nextflow/velocity/velocyto/nextflow.config
+++ b/target/nextflow/velocity/velocyto/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'velocity/velocyto'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Runs the velocity analysis on a BAM file, outputting a loom file.'
   author = 'Robrecht Cannoodt'
 }
diff --git a/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml b/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml
index 27f10fbb..38280e97 100644
--- a/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml
+++ b/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "celltypist"
 namespace: "workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -389,14 +389,14 @@ build_info:
   output: "target/nextflow/workflows/annotation/celltypist"
   executable: "target/nextflow/workflows/annotation/celltypist/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/_private/nextflow/workflows/rna/log_normalize"
   - "target/nextflow/annotate/celltypist"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -426,7 +426,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/annotation/celltypist/main.nf b/target/nextflow/workflows/annotation/celltypist/main.nf
index cc2f0f51..1a40f9bb 100644
--- a/target/nextflow/workflows/annotation/celltypist/main.nf
+++ b/target/nextflow/workflows/annotation/celltypist/main.nf
@@ -1,4 +1,4 @@
-// celltypist v4.0.0
+// celltypist v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "celltypist",
   "namespace" : "workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3517,12 +3517,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/celltypist",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3547,7 +3547,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/annotation/celltypist/nextflow.config b/target/nextflow/workflows/annotation/celltypist/nextflow.config
index 5941e33e..27fd9d55 100644
--- a/target/nextflow/workflows/annotation/celltypist/nextflow.config
+++ b/target/nextflow/workflows/annotation/celltypist/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/annotation/celltypist'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Cell type annotation workflow by performing lognormalization of the raw counts layer followed by cell type annotation with CellTypist.'
   author = 'Dorien Roosen, Weiwei Schultz'
 }
diff --git a/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml b/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml
index 6bc97006..4680cfed 100644
--- a/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml
+++ b/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "harmony_knn"
 namespace: "workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -444,7 +444,7 @@ build_info:
   output: "target/nextflow/workflows/annotation/harmony_knn"
   executable: "target/nextflow/workflows/annotation/harmony_knn/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/workflows/integration/harmony_leiden"
@@ -459,7 +459,7 @@ build_info:
   - "target/nextflow/dataflow/merge"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -489,7 +489,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/annotation/harmony_knn/main.nf b/target/nextflow/workflows/annotation/harmony_knn/main.nf
index 5b4fae4f..fcafb425 100644
--- a/target/nextflow/workflows/annotation/harmony_knn/main.nf
+++ b/target/nextflow/workflows/annotation/harmony_knn/main.nf
@@ -1,4 +1,4 @@
-// harmony_knn v4.0.0
+// harmony_knn v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "harmony_knn",
   "namespace" : "workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3596,12 +3596,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/harmony_knn",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3626,7 +3626,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3713,8 +3713,11 @@ workflow run_wf {
         )
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
-        
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         types.collect{ dat ->
           // def new_id = id + "_" + dat.name
           def new_id = id // it's okay because the channel will get split up anyways
@@ -3850,7 +3853,11 @@ workflow run_wf {
                 ]
                 return [id, new_state]
             }
-            def files = readCsv(state.output_files.toUriString())
+            def csv = state.output_files.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+            def header = csv.head()
+            def files = csv.tail().collect { row ->
+                [header, row].transpose().collectEntries()
+            }
             def query_file = files.findAll{ dat -> dat.name == 'query' }
             assert query_file.size() == 1, 'there should only be one query file'
             def reference_file = files.findAll{ dat -> dat.name == 'reference' }
diff --git a/target/nextflow/workflows/annotation/harmony_knn/nextflow.config b/target/nextflow/workflows/annotation/harmony_knn/nextflow.config
index d52b416d..18380958 100644
--- a/target/nextflow/workflows/annotation/harmony_knn/nextflow.config
+++ b/target/nextflow/workflows/annotation/harmony_knn/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/annotation/harmony_knn'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Cell type annotation workflow by performing harmony integration of reference and query dataset followed by KNN label transfer.'
   author = 'Dorien Roosen, Weiwei Schultz'
 }
diff --git a/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml b/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml
index d278c4fe..de770d66 100644
--- a/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml
+++ b/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanvi_scarches"
 namespace: "workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -558,7 +558,7 @@ build_info:
   output: "target/nextflow/workflows/annotation/scanvi_scarches"
   executable: "target/nextflow/workflows/annotation/scanvi_scarches/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/integrate/scvi"
@@ -567,7 +567,7 @@ build_info:
   - "target/nextflow/workflows/multiomics/neighbors_leiden_umap"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -597,7 +597,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/annotation/scanvi_scarches/main.nf b/target/nextflow/workflows/annotation/scanvi_scarches/main.nf
index 94a296b4..8b9a67ab 100644
--- a/target/nextflow/workflows/annotation/scanvi_scarches/main.nf
+++ b/target/nextflow/workflows/annotation/scanvi_scarches/main.nf
@@ -1,4 +1,4 @@
-// scanvi_scarches v4.0.0
+// scanvi_scarches v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scanvi_scarches",
   "namespace" : "workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3687,12 +3687,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/scanvi_scarches",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3717,7 +3717,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config b/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config
index 03a165df..712485b1 100644
--- a/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config
+++ b/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/annotation/scanvi_scarches'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Cell type annotation workflow using ScanVI with scArches for reference mapping.'
   author = 'Dorien Roosen, Weiwei Schultz'
 }
diff --git a/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml b/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml
index 56f89dfb..f856b572 100644
--- a/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml
+++ b/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvi_knn"
 namespace: "workflows/annotation"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -530,7 +530,7 @@ build_info:
   output: "target/nextflow/workflows/annotation/scvi_knn"
   executable: "target/nextflow/workflows/annotation/scvi_knn/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/workflows/integration/scvi_leiden"
@@ -544,7 +544,7 @@ build_info:
   - "target/nextflow/dataflow/merge"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -574,7 +574,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/annotation/scvi_knn/main.nf b/target/nextflow/workflows/annotation/scvi_knn/main.nf
index dcd77056..9d945fc6 100644
--- a/target/nextflow/workflows/annotation/scvi_knn/main.nf
+++ b/target/nextflow/workflows/annotation/scvi_knn/main.nf
@@ -1,4 +1,4 @@
-// scvi_knn v4.0.0
+// scvi_knn v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scvi_knn",
   "namespace" : "workflows/annotation",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3689,12 +3689,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/scvi_knn",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3719,7 +3719,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3808,7 +3808,11 @@ workflow run_wf {
       )
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         
         types.collect{ dat ->
           // def new_id = id + "_" + dat.name
@@ -3946,7 +3950,11 @@ workflow run_wf {
             ]
             return [id, new_state]
           }
-          def files = readCsv(state.output_files.toUriString())
+          def csv = state.output_files.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+          def header = csv.head()
+          def files = csv.tail().collect { row ->
+              [header, row].transpose().collectEntries()
+          }
           def query_file = files.findAll{ dat -> dat.name == 'query' }
           assert query_file.size() == 1, 'there should only be one query file'
           def reference_file = files.findAll{ dat -> dat.name == 'reference' }
diff --git a/target/nextflow/workflows/annotation/scvi_knn/nextflow.config b/target/nextflow/workflows/annotation/scvi_knn/nextflow.config
index 46c7b390..5d439777 100644
--- a/target/nextflow/workflows/annotation/scvi_knn/nextflow.config
+++ b/target/nextflow/workflows/annotation/scvi_knn/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/annotation/scvi_knn'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = '"Cell type annotation workflow that performs scVI integration of reference and query dataset followed by KNN label transfer. \nThe query and reference datasets are expected to be pre-processed in the same way, for example with the `process_samples` workflow of OpenPipeline.\nNote that this workflow will integrate the reference dataset from scratch and integrate the query dataset in the same embedding space. \nThe workflow does not currently output the trained SCVI reference model."\n'
   author = 'Dorien Roosen, Weiwei Schultz'
 }
diff --git a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml
index ca2d28df..8e03ea31 100644
--- a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml
+++ b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "pseudobulk_deseq2"
 namespace: "workflows/differential_expression"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Jakub Majercik"
   roles:
@@ -363,7 +363,7 @@ build_info:
   output: "target/nextflow/workflows/differential_expression/pseudobulk_deseq2"
   executable: "target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/differential_expression/create_pseudobulk"
@@ -374,7 +374,7 @@ build_info:
   - "target/nextflow/filter/do_filter"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -404,7 +404,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf
index cad45d98..d27bf294 100644
--- a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf
+++ b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf
@@ -1,4 +1,4 @@
-// pseudobulk_deseq2 v4.0.0
+// pseudobulk_deseq2 v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "pseudobulk_deseq2",
   "namespace" : "workflows/differential_expression",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Jakub Majercik",
@@ -3495,12 +3495,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/differential_expression/pseudobulk_deseq2",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3525,7 +3525,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config
index c4faa7ae..b5154f67 100644
--- a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config
+++ b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/differential_expression/pseudobulk_deseq2'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs pseudobulk generation and subsequent differential expression analysis using DESeq2.\n'
   author = 'Jakub Majercik, Weiwei Schultz'
 }
diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml b/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml
index f19db404..23fb8d47 100644
--- a/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml
+++ b/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "gdo_singlesample"
 namespace: "workflows/gdo"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -225,14 +225,14 @@ build_info:
   output: "target/nextflow/workflows/gdo/gdo_singlesample"
   executable: "target/nextflow/workflows/gdo/gdo_singlesample/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/filter/filter_with_counts"
   - "target/nextflow/filter/do_filter"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -262,7 +262,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/main.nf b/target/nextflow/workflows/gdo/gdo_singlesample/main.nf
index e9b71c30..6b1a40d6 100644
--- a/target/nextflow/workflows/gdo/gdo_singlesample/main.nf
+++ b/target/nextflow/workflows/gdo/gdo_singlesample/main.nf
@@ -1,4 +1,4 @@
-// gdo_singlesample v4.0.0
+// gdo_singlesample v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "gdo_singlesample",
   "namespace" : "workflows/gdo",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3327,12 +3327,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/gdo/gdo_singlesample",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3357,7 +3357,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config b/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config
index 4851e482..748fcab5 100644
--- a/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config
+++ b/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/gdo/gdo_singlesample'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Processing unimodal single-sample guide-derived oligonucleotide (GDO) data.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml b/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml
index cfeb4dcb..5140c331 100644
--- a/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml
+++ b/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bd_rhapsody"
 namespace: "workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Robrecht Cannoodt"
   roles:
@@ -609,14 +609,14 @@ build_info:
   output: "target/nextflow/workflows/ingestion/bd_rhapsody"
   executable: "target/nextflow/workflows/ingestion/bd_rhapsody/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/mapping/bd_rhapsody"
   - "target/nextflow/convert/from_bdrhap_to_h5mu"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -646,7 +646,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf b/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf
index 328ad1d4..0c19764d 100644
--- a/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf
+++ b/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf
@@ -1,4 +1,4 @@
-// bd_rhapsody v4.0.0
+// bd_rhapsody v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bd_rhapsody",
   "namespace" : "workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Robrecht Cannoodt",
@@ -3775,12 +3775,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/bd_rhapsody",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3805,7 +3805,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config b/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config
index 46b4d214..15b7dc2b 100644
--- a/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config
+++ b/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/ingestion/bd_rhapsody'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'BD Rhapsody Sequence Analysis CWL pipeline v2.2.1\n\nThis pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported\nsequencing libraries are those generated by the BD Rhapsody assay kits, including: Whole Transcriptome\nmRNA, Targeted mRNA, AbSeq Antibody-Oligonucleotides, Single-Cell Multiplexing, TCR/BCR, and\nATAC-Seq\n\nThe CWL pipeline file is obtained by cloning \'https://bitbucket.org/CRSwDev/cwl\' and removing all objects with class \'DockerRequirement\' from the YAML.\n'
   author = 'Robrecht Cannoodt, Dorien Roosen'
 }
diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml
index 58cc7a23..04951cd2 100644
--- a/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml
+++ b/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_mapping"
 namespace: "workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -324,7 +324,7 @@ build_info:
   output: "target/nextflow/workflows/ingestion/cellranger_mapping"
   executable: "target/nextflow/workflows/ingestion/cellranger_mapping/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/mapping/cellranger_count"
@@ -332,7 +332,7 @@ build_info:
   - "target/nextflow/convert/from_10xh5_to_h5mu"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -362,7 +362,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf b/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf
index 942d5833..b5d43e93 100644
--- a/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf
+++ b/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf
@@ -1,4 +1,4 @@
-// cellranger_mapping v4.0.0
+// cellranger_mapping v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_mapping",
   "namespace" : "workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3455,12 +3455,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/cellranger_mapping",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3485,7 +3485,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config
index a6e03ef2..490b3756 100644
--- a/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config
+++ b/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/ingestion/cellranger_mapping'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'A pipeline for running Cell Ranger mapping.'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer'
 }
diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml
index 0211fb9d..f3d81c77 100644
--- a/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml
+++ b/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_multi"
 namespace: "workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -907,14 +907,14 @@ build_info:
   output: "target/nextflow/workflows/ingestion/cellranger_multi"
   executable: "target/nextflow/workflows/ingestion/cellranger_multi/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/mapping/cellranger_multi"
   - "target/nextflow/convert/from_cellranger_multi_to_h5mu"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -944,7 +944,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/main.nf b/target/nextflow/workflows/ingestion/cellranger_multi/main.nf
index 703807aa..a7d8169a 100644
--- a/target/nextflow/workflows/ingestion/cellranger_multi/main.nf
+++ b/target/nextflow/workflows/ingestion/cellranger_multi/main.nf
@@ -1,4 +1,4 @@
-// cellranger_multi v4.0.0
+// cellranger_multi v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_multi",
   "namespace" : "workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3993,12 +3993,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/cellranger_multi",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -4023,7 +4023,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4169,7 +4169,11 @@ workflow run_wf {
   output_ch = h5mu_stub_ch.concat(h5mu_ch)
     | flatMap {id, state ->
       def h5mu_list = state.output_h5mu
-      def samples = readCsv(state.sample_csv.toUriString())
+      def csv = state.sample_csv.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+      def header = csv.head()
+      def samples = csv.tail().collect { row ->
+          [header, row].transpose().collectEntries()
+      }
       println "Samples: $samples" 
       def result = h5mu_list.collect{ h5mu_file ->
         println "H5mu: ${h5mu_file}, getName: ${h5mu_file.getName()}"
diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config
index 7ef20b09..7f78e952 100644
--- a/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config
+++ b/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/ingestion/cellranger_multi'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'A pipeline for running Cell Ranger multi.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml
index 2ece9975..225315b5 100644
--- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml
+++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "cellranger_postprocessing"
 namespace: "workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -234,7 +234,7 @@ build_info:
   output: "target/nextflow/workflows/ingestion/cellranger_postprocessing"
   executable: "target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/correction/cellbender_remove_background"
@@ -242,7 +242,7 @@ build_info:
   - "target/nextflow/filter/subset_h5mu"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -272,7 +272,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf b/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf
index 94d632e8..040a3ee9 100644
--- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf
+++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf
@@ -1,4 +1,4 @@
-// cellranger_postprocessing v4.0.0
+// cellranger_postprocessing v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "cellranger_postprocessing",
   "namespace" : "workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3357,12 +3357,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/cellranger_postprocessing",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3387,7 +3387,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config
index 7d01ee32..371a12d1 100644
--- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config
+++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/ingestion/cellranger_postprocessing'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Post-processing Cell Ranger datasets.'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml b/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml
index cdfab3da..a9f17c02 100644
--- a/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml
+++ b/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "conversion"
 namespace: "workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -210,7 +210,7 @@ build_info:
   output: "target/nextflow/workflows/ingestion/conversion"
   executable: "target/nextflow/workflows/ingestion/conversion/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/convert/from_10xh5_to_h5mu"
@@ -218,7 +218,7 @@ build_info:
   - "target/nextflow/convert/from_h5ad_to_h5mu"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -248,7 +248,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/ingestion/conversion/main.nf b/target/nextflow/workflows/ingestion/conversion/main.nf
index 2a913b2d..e2ceac3b 100644
--- a/target/nextflow/workflows/ingestion/conversion/main.nf
+++ b/target/nextflow/workflows/ingestion/conversion/main.nf
@@ -1,4 +1,4 @@
-// conversion v4.0.0
+// conversion v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "conversion",
   "namespace" : "workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3322,12 +3322,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/conversion",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3352,7 +3352,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/ingestion/conversion/nextflow.config b/target/nextflow/workflows/ingestion/conversion/nextflow.config
index 387001ba..a31d4379 100644
--- a/target/nextflow/workflows/ingestion/conversion/nextflow.config
+++ b/target/nextflow/workflows/ingestion/conversion/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/ingestion/conversion'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'A pipeline to convert different file formats to .h5mu.'
   author = 'Dries Schaumont, Dries De Maeyer'
 }
diff --git a/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml b/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml
index 8e79cf8d..52dd22a2 100644
--- a/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml
+++ b/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "demux"
 namespace: "workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Toni Verbeiren"
   roles:
@@ -293,7 +293,7 @@ build_info:
   output: "target/nextflow/workflows/ingestion/demux"
   executable: "target/nextflow/workflows/ingestion/demux/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/demux/cellranger_mkfastq"
@@ -303,7 +303,7 @@ build_info:
   - "target/nextflow/qc/multiqc"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -333,7 +333,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/ingestion/demux/main.nf b/target/nextflow/workflows/ingestion/demux/main.nf
index b25476d2..9961c73b 100644
--- a/target/nextflow/workflows/ingestion/demux/main.nf
+++ b/target/nextflow/workflows/ingestion/demux/main.nf
@@ -1,4 +1,4 @@
-// demux v4.0.0
+// demux v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3039,7 +3039,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "demux",
   "namespace" : "workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Toni Verbeiren",
@@ -3438,12 +3438,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/demux",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3468,7 +3468,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/ingestion/demux/nextflow.config b/target/nextflow/workflows/ingestion/demux/nextflow.config
index 8a181710..9ccd47ed 100644
--- a/target/nextflow/workflows/ingestion/demux/nextflow.config
+++ b/target/nextflow/workflows/ingestion/demux/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/ingestion/demux'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Convert `.bcl` files to `.fastq` files using bcl2fastq, bcl-convert or Cell Ranger mkfastq.\n'
   author = 'Toni Verbeiren, Marijke Van Moerbeke, Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt'
 }
diff --git a/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml b/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml
index 9deaec9f..e3ad98bd 100644
--- a/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml
+++ b/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "make_reference"
 namespace: "workflows/ingestion"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Angela Oliveira Pisco"
   roles:
@@ -395,7 +395,7 @@ build_info:
   output: "target/nextflow/workflows/ingestion/make_reference"
   executable: "target/nextflow/workflows/ingestion/make_reference/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/reference/make_reference"
@@ -405,7 +405,7 @@ build_info:
   - "target/nextflow/reference/build_cellranger_arc_reference"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -435,7 +435,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/ingestion/make_reference/main.nf b/target/nextflow/workflows/ingestion/make_reference/main.nf
index 6e970040..0881b157 100644
--- a/target/nextflow/workflows/ingestion/make_reference/main.nf
+++ b/target/nextflow/workflows/ingestion/make_reference/main.nf
@@ -1,4 +1,4 @@
-// make_reference v4.0.0
+// make_reference v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "make_reference",
   "namespace" : "workflows/ingestion",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Angela Oliveira Pisco",
@@ -3537,12 +3537,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/make_reference",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3567,7 +3567,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/ingestion/make_reference/nextflow.config b/target/nextflow/workflows/ingestion/make_reference/nextflow.config
index 37cb9e17..2ef0e8f5 100644
--- a/target/nextflow/workflows/ingestion/make_reference/nextflow.config
+++ b/target/nextflow/workflows/ingestion/make_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/ingestion/make_reference'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Build a transcriptomics reference into one of many formats.\n'
   author = 'Angela Oliveira Pisco, Robrecht Cannoodt, Weiwei Schultz'
 }
diff --git a/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml
index af9acecd..ea054550 100644
--- a/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bbknn_leiden"
 namespace: "workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Mauro Saporita"
   roles:
@@ -335,7 +335,7 @@ build_info:
   output: "target/nextflow/workflows/integration/bbknn_leiden"
   executable: "target/nextflow/workflows/integration/bbknn_leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/cluster/leiden"
@@ -344,7 +344,7 @@ build_info:
   - "target/nextflow/metadata/move_obsm_to_obs"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -374,7 +374,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/integration/bbknn_leiden/main.nf b/target/nextflow/workflows/integration/bbknn_leiden/main.nf
index 93c7233f..2484c5a6 100644
--- a/target/nextflow/workflows/integration/bbknn_leiden/main.nf
+++ b/target/nextflow/workflows/integration/bbknn_leiden/main.nf
@@ -1,4 +1,4 @@
-// bbknn_leiden v4.0.0
+// bbknn_leiden v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "bbknn_leiden",
   "namespace" : "workflows/integration",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Mauro Saporita",
@@ -3457,12 +3457,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/integration/bbknn_leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3487,7 +3487,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config b/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config
index 5ec3fdfd..65747c61 100644
--- a/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config
+++ b/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/integration/bbknn_leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Run bbknn followed by leiden clustering and run umap on the result.'
   author = 'Mauro Saporita, Povilas Gibas'
 }
diff --git a/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml
index 367ea2ef..3d1c8484 100644
--- a/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "harmony_leiden"
 namespace: "workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -363,7 +363,7 @@ build_info:
   output: "target/nextflow/workflows/integration/harmony_leiden"
   executable: "target/nextflow/workflows/integration/harmony_leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/integrate/harmonypy"
@@ -373,7 +373,7 @@ build_info:
   - "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -403,7 +403,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/integration/harmony_leiden/main.nf b/target/nextflow/workflows/integration/harmony_leiden/main.nf
index d8e02627..c00702ba 100644
--- a/target/nextflow/workflows/integration/harmony_leiden/main.nf
+++ b/target/nextflow/workflows/integration/harmony_leiden/main.nf
@@ -1,4 +1,4 @@
-// harmony_leiden v4.0.0
+// harmony_leiden v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "harmony_leiden",
   "namespace" : "workflows/integration",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3494,12 +3494,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/integration/harmony_leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3524,7 +3524,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/integration/harmony_leiden/nextflow.config b/target/nextflow/workflows/integration/harmony_leiden/nextflow.config
index 3622fd58..01f71a81 100644
--- a/target/nextflow/workflows/integration/harmony_leiden/nextflow.config
+++ b/target/nextflow/workflows/integration/harmony_leiden/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/integration/harmony_leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml
index 18089967..6d6be15c 100644
--- a/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scanorama_leiden"
 namespace: "workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Mauro Saporita"
   roles:
@@ -359,14 +359,14 @@ build_info:
   output: "target/nextflow/workflows/integration/scanorama_leiden"
   executable: "target/nextflow/workflows/integration/scanorama_leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/integrate/scanorama"
   - "target/nextflow/workflows/multiomics/neighbors_leiden_umap"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -396,7 +396,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/integration/scanorama_leiden/main.nf b/target/nextflow/workflows/integration/scanorama_leiden/main.nf
index 087a7879..530c1aa2 100644
--- a/target/nextflow/workflows/integration/scanorama_leiden/main.nf
+++ b/target/nextflow/workflows/integration/scanorama_leiden/main.nf
@@ -1,4 +1,4 @@
-// scanorama_leiden v4.0.0
+// scanorama_leiden v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scanorama_leiden",
   "namespace" : "workflows/integration",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Mauro Saporita",
@@ -3489,12 +3489,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/integration/scanorama_leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3519,7 +3519,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config b/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config
index d1c1719a..e0e44aa4 100644
--- a/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config
+++ b/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/integration/scanorama_leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result.'
   author = 'Mauro Saporita, Povilas Gibas'
 }
diff --git a/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml
index ded49514..c4d6c4bf 100644
--- a/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "scvi_leiden"
 namespace: "workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -486,7 +486,7 @@ build_info:
   output: "target/nextflow/workflows/integration/scvi_leiden"
   executable: "target/nextflow/workflows/integration/scvi_leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/integrate/scvi"
@@ -496,7 +496,7 @@ build_info:
   - "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -526,7 +526,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/integration/scvi_leiden/main.nf b/target/nextflow/workflows/integration/scvi_leiden/main.nf
index 2e470eec..8daaeb62 100644
--- a/target/nextflow/workflows/integration/scvi_leiden/main.nf
+++ b/target/nextflow/workflows/integration/scvi_leiden/main.nf
@@ -1,4 +1,4 @@
-// scvi_leiden v4.0.0
+// scvi_leiden v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "scvi_leiden",
   "namespace" : "workflows/integration",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3618,12 +3618,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/integration/scvi_leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3648,7 +3648,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/integration/scvi_leiden/nextflow.config b/target/nextflow/workflows/integration/scvi_leiden/nextflow.config
index f560d595..05657406 100644
--- a/target/nextflow/workflows/integration/scvi_leiden/nextflow.config
+++ b/target/nextflow/workflows/integration/scvi_leiden/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/integration/scvi_leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml
index 21082ffc..ae8ebd84 100644
--- a/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi_leiden"
 namespace: "workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dorien Roosen"
   roles:
@@ -414,14 +414,14 @@ build_info:
   output: "target/nextflow/workflows/integration/totalvi_leiden"
   executable: "target/nextflow/workflows/integration/totalvi_leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/integrate/totalvi"
   - "target/nextflow/workflows/multiomics/neighbors_leiden_umap"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -451,7 +451,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/integration/totalvi_leiden/main.nf b/target/nextflow/workflows/integration/totalvi_leiden/main.nf
index 620c129c..a7f9b6f9 100644
--- a/target/nextflow/workflows/integration/totalvi_leiden/main.nf
+++ b/target/nextflow/workflows/integration/totalvi_leiden/main.nf
@@ -1,4 +1,4 @@
-// totalvi_leiden v4.0.0
+// totalvi_leiden v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "totalvi_leiden",
   "namespace" : "workflows/integration",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dorien Roosen",
@@ -3533,12 +3533,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/integration/totalvi_leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3563,7 +3563,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config b/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config
index 4dfeea25..91cc1151 100644
--- a/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config
+++ b/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/integration/totalvi_leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Run totalVI integration, followed by neighbour calculations, leiden clustering and UMAP.'
   author = 'Dorien Roosen'
 }
diff --git a/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml
index d4db973c..05dfba5d 100644
--- a/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml
+++ b/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "totalvi_scarches_leiden"
 namespace: "workflows/integration"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -496,14 +496,14 @@ build_info:
   output: "target/nextflow/workflows/integration/totalvi_scarches_leiden"
   executable: "target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/integrate/totalvi_scarches"
   - "target/nextflow/workflows/multiomics/neighbors_leiden_umap"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -533,7 +533,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf b/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf
index 9a9f0a7c..de0f062d 100644
--- a/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf
+++ b/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf
@@ -1,4 +1,4 @@
-// totalvi_scarches_leiden v4.0.0
+// totalvi_scarches_leiden v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "totalvi_scarches_leiden",
   "namespace" : "workflows/integration",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3634,12 +3634,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/integration/totalvi_scarches_leiden",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3664,7 +3664,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config b/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config
index e0084d00..723fb10f 100644
--- a/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config
+++ b/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/integration/totalvi_scarches_leiden'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Run totalVI integration by mapping the query dataset to a reference, followed by neighbour calculations, leiden clustering and run umap on the result.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml b/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml
index 0c82a5a4..7aa5cab7 100644
--- a/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "dimensionality_reduction"
 namespace: "workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -278,14 +278,14 @@ build_info:
   output: "target/nextflow/workflows/multiomics/dimensionality_reduction"
   executable: "target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/dimred/pca"
   - "target/nextflow/workflows/multiomics/neighbors_leiden_umap"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -315,7 +315,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf b/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf
index cd8c1ef5..54b931ba 100644
--- a/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf
+++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf
@@ -1,4 +1,4 @@
-// dimensionality_reduction v4.0.0
+// dimensionality_reduction v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "dimensionality_reduction",
   "namespace" : "workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3390,12 +3390,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/dimensionality_reduction",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3420,7 +3420,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config b/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config
index 86befacf..ab1e05b1 100644
--- a/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config
+++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/dimensionality_reduction'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml
index 59ee7181..016f9f98 100644
--- a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "neighbors_leiden_umap"
 namespace: "workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -234,7 +234,7 @@ build_info:
   output: "target/nextflow/workflows/multiomics/neighbors_leiden_umap"
   executable: "target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/cluster/leiden"
@@ -243,7 +243,7 @@ build_info:
   - "target/nextflow/metadata/move_obsm_to_obs"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -273,7 +273,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf
index 0f946302..7ef3f235 100644
--- a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf
+++ b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf
@@ -1,4 +1,4 @@
-// neighbors_leiden_umap v4.0.0
+// neighbors_leiden_umap v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "neighbors_leiden_umap",
   "namespace" : "workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3331,12 +3331,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/neighbors_leiden_umap",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3361,7 +3361,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config
index 0469f20c..470198fe 100644
--- a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config
+++ b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/neighbors_leiden_umap'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Performs neighborhood search, leiden clustering and run umap on an integrated embedding.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml b/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml
index 2edfafa4..0b6a5225 100644
--- a/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "process_batches"
 namespace: "workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -380,7 +380,7 @@ build_info:
   output: "target/nextflow/workflows/multiomics/process_batches"
   executable: "target/nextflow/workflows/multiomics/process_batches/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/dataflow/merge"
@@ -392,7 +392,7 @@ build_info:
   - "target/nextflow/workflows/multiomics/dimensionality_reduction"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -422,7 +422,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/multiomics/process_batches/main.nf b/target/nextflow/workflows/multiomics/process_batches/main.nf
index 379df74b..ebcad2fb 100644
--- a/target/nextflow/workflows/multiomics/process_batches/main.nf
+++ b/target/nextflow/workflows/multiomics/process_batches/main.nf
@@ -1,4 +1,4 @@
-// process_batches v4.0.0
+// process_batches v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "process_batches",
   "namespace" : "workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3513,12 +3513,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/process_batches",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3543,7 +3543,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -3623,7 +3623,11 @@ workflow run_wf {
       // by reading the output csv (the csv contains 1 line per output file)
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         
         types.collect{ dat ->
           def new_id = state.original_id + "_${dat.name}" // Make a unique ID by appending the modality name.
diff --git a/target/nextflow/workflows/multiomics/process_batches/nextflow.config b/target/nextflow/workflows/multiomics/process_batches/nextflow.config
index feff87cc..f77ae890 100644
--- a/target/nextflow/workflows/multiomics/process_batches/nextflow.config
+++ b/target/nextflow/workflows/multiomics/process_batches/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/process_batches'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'This workflow serves as an entrypoint into the \'full_pipeline\' in order to\nre-run the multisample processing and the integration setup. An input .h5mu file will \nfirst be split in order to run the multisample processing per modality. Next, the modalities\nare merged again and the integration setup pipeline is executed. Please note that this workflow\nassumes that samples from multiple pipelines are already concatenated. \n'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml
index 68b70f68..8168b5d7 100644
--- a/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml
+++ b/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "process_samples"
 namespace: "workflows/multiomics"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -711,7 +711,7 @@ build_info:
   output: "target/nextflow/workflows/multiomics/process_samples"
   executable: "target/nextflow/workflows/multiomics/process_samples/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/metadata/add_id"
@@ -724,7 +724,7 @@ build_info:
   - "target/nextflow/workflows/multiomics/process_batches"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -754,7 +754,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/multiomics/process_samples/main.nf b/target/nextflow/workflows/multiomics/process_samples/main.nf
index a35e97a7..068943c9 100644
--- a/target/nextflow/workflows/multiomics/process_samples/main.nf
+++ b/target/nextflow/workflows/multiomics/process_samples/main.nf
@@ -1,4 +1,4 @@
-// process_samples v4.0.0
+// process_samples v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "process_samples",
   "namespace" : "workflows/multiomics",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3916,12 +3916,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/process_samples",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3946,7 +3946,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
@@ -4033,7 +4033,11 @@ workflow run_wf {
       )
       | flatMap {id, state ->
         def outputDir = state.output
-        def types = readCsv(state.output_types.toUriString())
+        def csv = state.output_types.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")}
+        def header = csv.head()
+        def types = csv.tail().collect { row ->
+            [header, row].transpose().collectEntries()
+        }
         
         types.collect{ dat ->
           // def new_id = id + "_" + dat.name
diff --git a/target/nextflow/workflows/multiomics/process_samples/nextflow.config b/target/nextflow/workflows/multiomics/process_samples/nextflow.config
index 17b39a54..e6c13878 100644
--- a/target/nextflow/workflows/multiomics/process_samples/nextflow.config
+++ b/target/nextflow/workflows/multiomics/process_samples/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/multiomics/process_samples'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'A pipeline to analyse multiple multiomics samples.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml b/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml
index be617202..953d7cb1 100644
--- a/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml
+++ b/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "prot_multisample"
 namespace: "workflows/prot"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -284,14 +284,14 @@ build_info:
   output: "target/nextflow/workflows/prot/prot_multisample"
   executable: "target/nextflow/workflows/prot/prot_multisample/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/transform/clr"
   - "target/nextflow/workflows/qc/qc"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -321,7 +321,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/prot/prot_multisample/main.nf b/target/nextflow/workflows/prot/prot_multisample/main.nf
index c1be0812..99617f7e 100644
--- a/target/nextflow/workflows/prot/prot_multisample/main.nf
+++ b/target/nextflow/workflows/prot/prot_multisample/main.nf
@@ -1,4 +1,4 @@
-// prot_multisample v4.0.0
+// prot_multisample v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "prot_multisample",
   "namespace" : "workflows/prot",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3384,12 +3384,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/prot/prot_multisample",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3414,7 +3414,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/prot/prot_multisample/nextflow.config b/target/nextflow/workflows/prot/prot_multisample/nextflow.config
index f3bf4b51..b284929b 100644
--- a/target/nextflow/workflows/prot/prot_multisample/nextflow.config
+++ b/target/nextflow/workflows/prot/prot_multisample/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/prot/prot_multisample'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Processing unimodal multi-sample ADT data.'
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml b/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml
index 533c8bfe..e30a6cc8 100644
--- a/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml
+++ b/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "prot_singlesample"
 namespace: "workflows/prot"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -255,14 +255,14 @@ build_info:
   output: "target/nextflow/workflows/prot/prot_singlesample"
   executable: "target/nextflow/workflows/prot/prot_singlesample/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/filter/filter_with_counts"
   - "target/nextflow/filter/do_filter"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -292,7 +292,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/prot/prot_singlesample/main.nf b/target/nextflow/workflows/prot/prot_singlesample/main.nf
index 7cc6b238..ebf1b7a4 100644
--- a/target/nextflow/workflows/prot/prot_singlesample/main.nf
+++ b/target/nextflow/workflows/prot/prot_singlesample/main.nf
@@ -1,4 +1,4 @@
-// prot_singlesample v4.0.0
+// prot_singlesample v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "prot_singlesample",
   "namespace" : "workflows/prot",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3378,12 +3378,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/prot/prot_singlesample",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3408,7 +3408,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/prot/prot_singlesample/nextflow.config b/target/nextflow/workflows/prot/prot_singlesample/nextflow.config
index 7dc56ca7..48075db7 100644
--- a/target/nextflow/workflows/prot/prot_singlesample/nextflow.config
+++ b/target/nextflow/workflows/prot/prot_singlesample/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/prot/prot_singlesample'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Processing unimodal single-sample CITE-seq data.'
   author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/qc/qc/.config.vsh.yaml b/target/nextflow/workflows/qc/qc/.config.vsh.yaml
index f6268a38..c847e91c 100644
--- a/target/nextflow/workflows/qc/qc/.config.vsh.yaml
+++ b/target/nextflow/workflows/qc/qc/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "qc"
 namespace: "workflows/qc"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -364,14 +364,14 @@ build_info:
   output: "target/nextflow/workflows/qc/qc"
   executable: "target/nextflow/workflows/qc/qc/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/metadata/grep_annotation_column"
   - "target/nextflow/qc/calculate_qc_metrics"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -401,7 +401,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/qc/qc/main.nf b/target/nextflow/workflows/qc/qc/main.nf
index 53db6d5f..158323c1 100644
--- a/target/nextflow/workflows/qc/qc/main.nf
+++ b/target/nextflow/workflows/qc/qc/main.nf
@@ -1,4 +1,4 @@
-// qc v4.0.0
+// qc v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "qc",
   "namespace" : "workflows/qc",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3471,12 +3471,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/qc/qc",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3501,7 +3501,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/qc/qc/nextflow.config b/target/nextflow/workflows/qc/qc/nextflow.config
index d9abf287..81668e63 100644
--- a/target/nextflow/workflows/qc/qc/nextflow.config
+++ b/target/nextflow/workflows/qc/qc/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/qc/qc'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'A pipeline to add basic qc statistics to a MuData '
   author = 'Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml b/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml
index ce7fb90c..4c23e33a 100644
--- a/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml
+++ b/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rna_multisample"
 namespace: "workflows/rna"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -422,7 +422,7 @@ build_info:
   output: "target/nextflow/workflows/rna/rna_multisample"
   executable: "target/nextflow/workflows/rna/rna_multisample/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/feature_annotation/highly_variable_features_scanpy"
@@ -432,7 +432,7 @@ build_info:
   - "target/_private/nextflow/workflows/rna/log_normalize"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -462,7 +462,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/rna/rna_multisample/main.nf b/target/nextflow/workflows/rna/rna_multisample/main.nf
index cd3e2126..ac48dd2a 100644
--- a/target/nextflow/workflows/rna/rna_multisample/main.nf
+++ b/target/nextflow/workflows/rna/rna_multisample/main.nf
@@ -1,4 +1,4 @@
-// rna_multisample v4.0.0
+// rna_multisample v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "rna_multisample",
   "namespace" : "workflows/rna",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3557,12 +3557,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/rna/rna_multisample",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3587,7 +3587,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/rna/rna_multisample/nextflow.config b/target/nextflow/workflows/rna/rna_multisample/nextflow.config
index 3618c964..cc91db15 100644
--- a/target/nextflow/workflows/rna/rna_multisample/nextflow.config
+++ b/target/nextflow/workflows/rna/rna_multisample/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/rna/rna_multisample'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Processing unimodal multi-sample RNA transcriptomics data.'
   author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont'
 }
diff --git a/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml b/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml
index 7c113752..f89fd14b 100644
--- a/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml
+++ b/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rna_singlesample"
 namespace: "workflows/rna"
-version: "v4.0.0"
+version: "v4.0.1"
 authors:
 - name: "Dries De Maeyer"
   roles:
@@ -396,7 +396,7 @@ build_info:
   output: "target/nextflow/workflows/rna/rna_singlesample"
   executable: "target/nextflow/workflows/rna/rna_singlesample/main.nf"
   viash_version: "0.9.4"
-  git_commit: "de02293c9e13198622b988dac952b2c8c70a1e35"
+  git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92"
   git_remote: "https://github.com/openpipelines-bio/openpipeline"
   dependencies:
   - "target/nextflow/filter/filter_with_counts"
@@ -406,7 +406,7 @@ build_info:
   - "target/nextflow/workflows/qc/qc"
 package_config:
   name: "openpipeline"
-  version: "v4.0.0"
+  version: "v4.0.1"
   summary: "Best-practice workflows for single-cell multi-omics analyses.\n"
   description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\
     \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\
@@ -436,7 +436,7 @@ package_config:
     )'"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
   keywords:
   - "single-cell"
   - "multimodal"
diff --git a/target/nextflow/workflows/rna/rna_singlesample/main.nf b/target/nextflow/workflows/rna/rna_singlesample/main.nf
index 039779e0..282159f3 100644
--- a/target/nextflow/workflows/rna/rna_singlesample/main.nf
+++ b/target/nextflow/workflows/rna/rna_singlesample/main.nf
@@ -1,4 +1,4 @@
-// rna_singlesample v4.0.0
+// rna_singlesample v4.0.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3037,7 +3037,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "rna_singlesample",
   "namespace" : "workflows/rna",
-  "version" : "v4.0.0",
+  "version" : "v4.0.1",
   "authors" : [
     {
       "name" : "Dries De Maeyer",
@@ -3541,12 +3541,12 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/rna/rna_singlesample",
     "viash_version" : "0.9.4",
-    "git_commit" : "de02293c9e13198622b988dac952b2c8c70a1e35",
+    "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92",
     "git_remote" : "https://github.com/openpipelines-bio/openpipeline"
   },
   "package_config" : {
     "name" : "openpipeline",
-    "version" : "v4.0.0",
+    "version" : "v4.0.1",
     "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n",
     "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n  * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n  * Ingestion: Read mapping and generating a count matrix.\n  * Single sample processing: cell filtering and doublet detection.\n  * Multisample processing: Count transformation, normalization, QC metric calulations.\n  * Integration: Clustering, integration and batch correction using single and multimodal methods.\n  * Downstream analysis workflows\n",
     "info" : {
@@ -3571,7 +3571,7 @@ meta = [
       ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v4.0.0'"
+      ".engines[.type == 'docker'].target_tag := 'v4.0.1'"
     ],
     "keywords" : [
       "single-cell",
diff --git a/target/nextflow/workflows/rna/rna_singlesample/nextflow.config b/target/nextflow/workflows/rna/rna_singlesample/nextflow.config
index 2cc9f1c9..ed45fb90 100644
--- a/target/nextflow/workflows/rna/rna_singlesample/nextflow.config
+++ b/target/nextflow/workflows/rna/rna_singlesample/nextflow.config
@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/rna/rna_singlesample'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v4.0.0'
+  version = 'v4.0.1'
   description = 'Processing unimodal single-sample RNA transcriptomics data.'
   author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont'
 }