diff --git a/src/utils/save_params/config.vsh.yaml b/src/utils/save_params/config.vsh.yaml
index b4e10d12..2f6ff865 100644
--- a/src/utils/save_params/config.vsh.yaml
+++ b/src/utils/save_params/config.vsh.yaml
@@ -1,7 +1,7 @@
 name: save_params
 namespace: utils
 description: |
-  Save parameters to a file
+  Save parameters to a YAML file
 
 argument_groups:
   - name: Inputs
@@ -13,7 +13,7 @@ argument_groups:
         required: true
       - name: "--params_yaml"
         description: |
-          base64 encoded yaml file containing the state
+          base64 encoded yaml containing the state
         type: string
         required: true
     
@@ -21,9 +21,10 @@ argument_groups:
     arguments:
       - name: "--output"
         description: |
-          The output file
+          The output YAML file
         type: string
         required: true
+        example: "output.yaml"
 
 resources:
   - type: python_script
diff --git a/src/utils/save_params/script.py b/src/utils/save_params/script.py
index 7d427116..c7652c94 100644
--- a/src/utils/save_params/script.py
+++ b/src/utils/save_params/script.py
@@ -15,39 +15,24 @@ class Dumper(yaml.Dumper):
         return super(Dumper, self).increase_indent(flow, False)
 
 def decode_params_yaml(encoded_yaml):
-    # Step 1: Decode from Base64
     yaml_bytes = base64.b64decode(encoded_yaml)
-    
-    # Step 2: Convert bytes to string
     yaml_string = yaml_bytes.decode('utf-8')
-    
-    # Step 3: Extract pattern for Java path objects
-    # Find pattern: !!sun.nio.fs.UnixPath /path/to/file
-    pattern = r'!!sun\.nio\.fs\.UnixPath\s+([^\n]+)'
-    
-    # Replace with the actual path string (captured group)
-    yaml_string = re.sub(pattern, r'\1', yaml_string)
-    
-    # Handle any remaining empty UnixPath objects
-    yaml_string = yaml_string.replace('!!sun.nio.fs.UnixPath {}', '""')
-    
-    # Step 4: Parse YAML
     yaml_data = yaml.safe_load(yaml_string)
     
     return yaml_data
 
-def replace_id(value, sample_id):
-    if isinstance(value, str):
-        return value.replace('$id', sample_id)
-    elif isinstance(value, list):
-        return [replace_id(item, sample_id) for item in value]
-    return value
+# def replace_id(value, sample_id):
+#     if isinstance(value, str):
+#         return value.replace('$id', sample_id)
+#     elif isinstance(value, list):
+#         return [replace_id(item, sample_id) for item in value]
+#     return value
 
 print(par['params_yaml'])
 
 params = decode_params_yaml(par['params_yaml'])
-for key, value in params.items():
-    params[key] = replace_id(value, par["id"])
+# for key, value in params.items():
+#     params[key] = replace_id(value, par["id"])
 
 with open(par["output"], 'w') as f:
     yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)
diff --git a/src/workflows/htrnaseq/config.vsh.yaml b/src/workflows/htrnaseq/config.vsh.yaml
index beb72585..31eefc80 100644
--- a/src/workflows/htrnaseq/config.vsh.yaml
+++ b/src/workflows/htrnaseq/config.vsh.yaml
@@ -88,6 +88,11 @@ argument_groups:
         direction: output
         required: true
         default: report.$id.html
+      - name: "--params"
+        type: file
+        direction: output
+        required: true
+        default: params.$id.yaml
 resources:
   - type: nextflow_script
     path: main.nf
diff --git a/src/workflows/htrnaseq/main.nf b/src/workflows/htrnaseq/main.nf
index e8db6574..210fc71b 100644
--- a/src/workflows/htrnaseq/main.nf
+++ b/src/workflows/htrnaseq/main.nf
@@ -11,14 +11,6 @@ workflow run_wf {
         return [id, newState]
       }
 
-    // The featureData only has one requirement: the genome annotation.
-    // It can be generated straight away. Most of the time, there is one shared 
-    // annotation for all of the inputs and the fData should only be calculated once.
-    // The state is manpulated in such a way that there is one event created per unique
-    // input annotation file. In turn, the featureData file can joined into the original input
-    // channel which allows it to be shared across events if required.
-    f_data_ch = input_ch
-
       | save_params.run(
         fromState: {id, state ->
           // Define the function before using it
@@ -26,8 +18,10 @@ workflow run_wf {
           convertPaths = { value ->
             if (value instanceof java.nio.file.Path)
               return value.toUriString()
-            else if (value instanceof Collection)
+            else if (value instanceof List)
               return value.collect { convertPaths(it) }
+            else if (value instanceof Collection)
+              throw new UnsupportedOperationException("Collections other than Lists are not supported")
             else
               return value
           }
@@ -42,12 +36,21 @@ workflow run_wf {
           return [
             "id": id,
             "params_yaml": encodedYaml,
-            "output": "${id}_parameters.yaml"
+            "output": "params"
           ]
         },
-        toState: ["parameters": "output"]
+        toState: ["params": "output"]
       )
 
+    // The featureData only has one requirement: the genome annotation.
+    // It can be generated straight away. Most of the time, there is one shared 
+    // annotation for all of the inputs and the fData should only be calculated once.
+    // The state is manpulated in such a way that there is one event created per unique
+    // input annotation file. In turn, the featureData file can joined into the original input
+    // channel which allows it to be shared across events if required.
+    f_data_ch = input_ch
+
+
       | toSortedList()
       | flatMap {ids_and_states ->
         def annotation_files = ids_and_states.inject([:]){ old_state, id_and_state ->
@@ -347,7 +350,7 @@ workflow run_wf {
         "f_data": "f_data",
         "p_data": "p_data",
         "html_report": "html_report",
-        "parameters": "parameters",
+        "params": "params",
         "_meta": "_meta",
       ])
 
diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml
index f3bb1168..ae06a47e 100644
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -203,7 +203,7 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset
index d8f64059..0015a8ef 100755
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:02Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml
index b5e6063b..b698e91f 100644
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -180,7 +180,7 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata
index 11d7aab3..29f55837 100755
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:02Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml
index e44ed42b..1d6b96ae 100644
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -194,7 +194,7 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata
index 36a73b0c..14294602 100755
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:03Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 20189b2a..1054a554 100644
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -152,7 +152,7 @@ build_info:
   output: "target/executable/integration_test_components/htrnaseq/check_eset"
   executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
index 461dbd8d..b645545d 100755
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:01Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index 04c23325..8e114c10 100644
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -161,7 +161,7 @@ build_info:
   output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
index 1e346d22..d3f4a076 100755
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:03Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml
index 088a05e3..bdf0d1f3 100644
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -136,7 +136,7 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs
index 8a592f25..47f7e974 100755
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:01Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml
index 7d15aa62..88a00b18 100644
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results
index 28b140f5..9284391e 100755
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:02Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml
index aade00cf..e039befc 100644
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -282,7 +282,7 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map
index de6be21f..ca2e67f0 100755
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:03Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml
index ff359083..56e62b17 100644
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -206,7 +206,7 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report
index 3cece068..97e765c5 100755
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -462,9 +462,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:03Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml
index 6e5187d3..e6e798c2 100644
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
   output: "target/executable/stats/combine_star_logs"
   executable: "target/executable/stats/combine_star_logs/combine_star_logs"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs
index 710ab7e6..a516c3fd 100755
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:01Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
index e60fabf7..afcb7cda 100644
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
   output: "target/executable/stats/generate_pool_statistics"
   executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
index fcff8f89..3c2dab19 100755
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:02Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
index 4fdc4bb8..bb65cc0a 100644
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,7 +267,7 @@ build_info:
   output: "target/executable/stats/generate_well_statistics"
   executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics
index 61461805..b6df55c4 100755
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -461,9 +461,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:01Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml
index 41814f40..b2dacc4e 100644
--- a/target/executable/utils/save_params/.config.vsh.yaml
+++ b/target/executable/utils/save_params/.config.vsh.yaml
@@ -14,7 +14,7 @@ argument_groups:
     multiple_sep: ";"
   - type: "string"
     name: "--params_yaml"
-    description: "base64 encoded yaml file containing the state\n"
+    description: "base64 encoded yaml containing the state\n"
     info: null
     required: true
     direction: "input"
@@ -24,8 +24,10 @@ argument_groups:
   arguments:
   - type: "string"
     name: "--output"
-    description: "The output file\n"
+    description: "The output YAML file\n"
     info: null
+    example:
+    - "output.yaml"
     required: true
     direction: "input"
     multiple: false
@@ -37,7 +39,7 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
-description: "Save parameters to a file\n"
+description: "Save parameters to a YAML file\n"
 info: null
 status: "enabled"
 scope:
@@ -144,7 +146,7 @@ build_info:
   output: "target/executable/utils/save_params"
   executable: "target/executable/utils/save_params/save_params"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/utils/save_params/save_params b/target/executable/utils/save_params/save_params
index 04a574bf..446bb80e 100755
--- a/target/executable/utils/save_params/save_params
+++ b/target/executable/utils/save_params/save_params
@@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "pyyaml"
 
 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2025-04-01T15:16:03Z"
+LABEL org.opencontainers.image.created="2025-04-03T13:19:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+LABEL org.opencontainers.image.revision="24e6d49c099294ef0cedbe2666fdf64e21aad0df"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 function ViashHelp {
   echo "save_params save-params"
   echo ""
-  echo "Save parameters to a file"
+  echo "Save parameters to a YAML file"
   echo ""
   echo "Inputs:"
   echo "    --id"
@@ -584,12 +584,13 @@ function ViashHelp {
   echo ""
   echo "    --params_yaml"
   echo "        type: string, required parameter"
-  echo "        base64 encoded yaml file containing the state"
+  echo "        base64 encoded yaml containing the state"
   echo ""
   echo "Outputs:"
   echo "    --output"
   echo "        type: string, required parameter"
-  echo "        The output file"
+  echo "        example: output.yaml"
+  echo "        The output YAML file"
   echo ""
   echo "Viash built in Computational Requirements:"
   echo "    ---cpus=INT"
@@ -1078,39 +1079,24 @@ class Dumper(yaml.Dumper):
         return super(Dumper, self).increase_indent(flow, False)
 
 def decode_params_yaml(encoded_yaml):
-    # Step 1: Decode from Base64
     yaml_bytes = base64.b64decode(encoded_yaml)
-    
-    # Step 2: Convert bytes to string
     yaml_string = yaml_bytes.decode('utf-8')
-    
-    # Step 3: Extract pattern for Java path objects
-    # Find pattern: !!sun.nio.fs.UnixPath /path/to/file
-    pattern = r'!!sun\\.nio\\.fs\\.UnixPath\\s+([^\\n]+)'
-    
-    # Replace with the actual path string (captured group)
-    yaml_string = re.sub(pattern, r'\\1', yaml_string)
-    
-    # Handle any remaining empty UnixPath objects
-    yaml_string = yaml_string.replace('!!sun.nio.fs.UnixPath {}', '""')
-    
-    # Step 4: Parse YAML
     yaml_data = yaml.safe_load(yaml_string)
     
     return yaml_data
 
-def replace_id(value, sample_id):
-    if isinstance(value, str):
-        return value.replace('\$id', sample_id)
-    elif isinstance(value, list):
-        return [replace_id(item, sample_id) for item in value]
-    return value
+# def replace_id(value, sample_id):
+#     if isinstance(value, str):
+#         return value.replace('\$id', sample_id)
+#     elif isinstance(value, list):
+#         return [replace_id(item, sample_id) for item in value]
+#     return value
 
 print(par['params_yaml'])
 
 params = decode_params_yaml(par['params_yaml'])
-for key, value in params.items():
-    params[key] = replace_id(value, par["id"])
+# for key, value in params.items():
+#     params[key] = replace_id(value, par["id"])
 
 with open(par["output"], 'w') as f:
     yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)
diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml
index 2797a480..68503405 100644
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -203,7 +203,7 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf
index 0c651b43..56eda437 100644
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3309,7 +3309,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml
index 5b63f0fc..d0ad2a7d 100644
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -180,7 +180,7 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf
index e619c609..3fd1d3a8 100644
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3279,7 +3279,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml
index 4edefbb6..47dc204a 100644
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -194,7 +194,7 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf
index a8a4e5d2..6fc3fc75 100644
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3293,7 +3293,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 7edbdadf..a6da49f3 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -152,7 +152,7 @@ build_info:
   output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
   executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
index 2d4cbeb7..cc64ba5e 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -3233,7 +3233,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index 793bfb78..d0aba7ae 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -161,7 +161,7 @@ build_info:
   output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
index 3f91b91e..ef3b2eaf 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -3244,7 +3244,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
index 59bdb7fc..fe49d28f 100644
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -136,7 +136,7 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf
index 5fc9c574..4dc5dceb 100644
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -3207,7 +3207,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml
index cc62645b..183f1505 100644
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf
index 40da8e35..bbe4d0ad 100644
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3267,7 +3267,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml
index 9040c8cb..59a875a8 100644
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -282,7 +282,7 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf
index 58e342a4..0ff24c0a 100644
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3379,7 +3379,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml
index c165fddc..189373ef 100644
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -206,7 +206,7 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf
index debf1b06..14123875 100644
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3314,7 +3314,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
index 1aedebd2..fa48e80c 100644
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
   output: "target/nextflow/stats/combine_star_logs"
   executable: "target/nextflow/stats/combine_star_logs/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf
index 516c3dfe..2d38ec95 100644
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3295,7 +3295,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
index cab4f731..30d74315 100644
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
   output: "target/nextflow/stats/generate_pool_statistics"
   executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf
index c5ae1fd5..6d148ab4 100644
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3279,7 +3279,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
index aecc5814..c0f99931 100644
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,7 +267,7 @@ build_info:
   output: "target/nextflow/stats/generate_well_statistics"
   executable: "target/nextflow/stats/generate_well_statistics/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf
index a1854080..24f5928c 100644
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3374,7 +3374,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml
index adc74775..4e7116f1 100644
--- a/target/nextflow/utils/concatRuns/.config.vsh.yaml
+++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml
@@ -157,7 +157,7 @@ build_info:
   output: "target/nextflow/utils/concatRuns"
   executable: "target/nextflow/utils/concatRuns/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf
index 4c487f74..8ef1c1f7 100644
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,7 +3229,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml
index 778cba7f..058239f1 100644
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -168,7 +168,7 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf
index aa408222..b1ef6efc 100644
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3239,7 +3239,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml
index 6230ae48..efbc6fc1 100644
--- a/target/nextflow/utils/save_params/.config.vsh.yaml
+++ b/target/nextflow/utils/save_params/.config.vsh.yaml
@@ -14,7 +14,7 @@ argument_groups:
     multiple_sep: ";"
   - type: "string"
     name: "--params_yaml"
-    description: "base64 encoded yaml file containing the state\n"
+    description: "base64 encoded yaml containing the state\n"
     info: null
     required: true
     direction: "input"
@@ -24,8 +24,10 @@ argument_groups:
   arguments:
   - type: "string"
     name: "--output"
-    description: "The output file\n"
+    description: "The output YAML file\n"
     info: null
+    example:
+    - "output.yaml"
     required: true
     direction: "input"
     multiple: false
@@ -37,7 +39,7 @@ resources:
 - type: "file"
   path: "nextflow_labels.config"
   dest: "nextflow_labels.config"
-description: "Save parameters to a file\n"
+description: "Save parameters to a YAML file\n"
 info: null
 status: "enabled"
 scope:
@@ -144,7 +146,7 @@ build_info:
   output: "target/nextflow/utils/save_params"
   executable: "target/nextflow/utils/save_params/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/utils/save_params/main.nf b/target/nextflow/utils/save_params/main.nf
index 94b24e58..69d7f529 100644
--- a/target/nextflow/utils/save_params/main.nf
+++ b/target/nextflow/utils/save_params/main.nf
@@ -3054,7 +3054,7 @@ meta = [
         {
           "type" : "string",
           "name" : "--params_yaml",
-          "description" : "base64 encoded yaml file containing the state\n",
+          "description" : "base64 encoded yaml containing the state\n",
           "required" : true,
           "direction" : "input",
           "multiple" : false,
@@ -3068,7 +3068,10 @@ meta = [
         {
           "type" : "string",
           "name" : "--output",
-          "description" : "The output file\n",
+          "description" : "The output YAML file\n",
+          "example" : [
+            "output.yaml"
+          ],
           "required" : true,
           "direction" : "input",
           "multiple" : false,
@@ -3089,7 +3092,7 @@ meta = [
       "dest" : "nextflow_labels.config"
     }
   ],
-  "description" : "Save parameters to a file\n",
+  "description" : "Save parameters to a YAML file\n",
   "status" : "enabled",
   "scope" : {
     "image" : "public",
@@ -3218,7 +3221,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/utils/save_params",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
@@ -3311,39 +3314,24 @@ class Dumper(yaml.Dumper):
         return super(Dumper, self).increase_indent(flow, False)
 
 def decode_params_yaml(encoded_yaml):
-    # Step 1: Decode from Base64
     yaml_bytes = base64.b64decode(encoded_yaml)
-    
-    # Step 2: Convert bytes to string
     yaml_string = yaml_bytes.decode('utf-8')
-    
-    # Step 3: Extract pattern for Java path objects
-    # Find pattern: !!sun.nio.fs.UnixPath /path/to/file
-    pattern = r'!!sun\\\\.nio\\\\.fs\\\\.UnixPath\\\\s+([^\\\\n]+)'
-    
-    # Replace with the actual path string (captured group)
-    yaml_string = re.sub(pattern, r'\\\\1', yaml_string)
-    
-    # Handle any remaining empty UnixPath objects
-    yaml_string = yaml_string.replace('!!sun.nio.fs.UnixPath {}', '""')
-    
-    # Step 4: Parse YAML
     yaml_data = yaml.safe_load(yaml_string)
     
     return yaml_data
 
-def replace_id(value, sample_id):
-    if isinstance(value, str):
-        return value.replace('\\$id', sample_id)
-    elif isinstance(value, list):
-        return [replace_id(item, sample_id) for item in value]
-    return value
+# def replace_id(value, sample_id):
+#     if isinstance(value, str):
+#         return value.replace('\\$id', sample_id)
+#     elif isinstance(value, list):
+#         return [replace_id(item, sample_id) for item in value]
+#     return value
 
 print(par['params_yaml'])
 
 params = decode_params_yaml(par['params_yaml'])
-for key, value in params.items():
-    params[key] = replace_id(value, par["id"])
+# for key, value in params.items():
+#     params[key] = replace_id(value, par["id"])
 
 with open(par["output"], 'w') as f:
     yaml.dump(params, f, default_flow_style=False, Dumper=Dumper)
diff --git a/target/nextflow/utils/save_params/nextflow.config b/target/nextflow/utils/save_params/nextflow.config
index e83796cb..41085dcb 100644
--- a/target/nextflow/utils/save_params/nextflow.config
+++ b/target/nextflow/utils/save_params/nextflow.config
@@ -3,7 +3,7 @@ manifest {
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
   version = 'save-params'
-  description = 'Save parameters to a file\n'
+  description = 'Save parameters to a YAML file\n'
 }
 
 process.container = 'nextflow/bash:latest'
diff --git a/target/nextflow/utils/save_params/nextflow_schema.json b/target/nextflow/utils/save_params/nextflow_schema.json
index 39a26fa5..8e32c1ad 100644
--- a/target/nextflow/utils/save_params/nextflow_schema.json
+++ b/target/nextflow/utils/save_params/nextflow_schema.json
@@ -1,7 +1,7 @@
 {
 "$schema": "http://json-schema.org/draft-07/schema",
 "title": "save_params",
-"description": "Save parameters to a file\n",
+"description": "Save parameters to a YAML file\n",
 "type": "object",
 "definitions": {
 
@@ -27,8 +27,8 @@
                 "params_yaml": {
                 "type":
                 "string",
-                "description": "Type: `string`, required. base64 encoded yaml file containing the state\n",
-                "help_text": "Type: `string`, required. base64 encoded yaml file containing the state\n"
+                "description": "Type: `string`, required. base64 encoded yaml containing the state\n",
+                "help_text": "Type: `string`, required. base64 encoded yaml containing the state\n"
             
             }
     
@@ -47,8 +47,8 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `string`, required. The output file\n",
-                "help_text": "Type: `string`, required. The output file\n"
+                "description": "Type: `string`, required, example: `output.yaml`. The output YAML file\n",
+                "help_text": "Type: `string`, required, example: `output.yaml`. The output YAML file\n"
             
             }
     
diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
index 13481ab4..12cfb45c 100644
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -183,6 +183,17 @@ argument_groups:
     direction: "output"
     multiple: false
     multiple_sep: ";"
+  - type: "file"
+    name: "--params"
+    info: null
+    default:
+    - "params.$id.yaml"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
 resources:
 - type: "nextflow_script"
   path: "main.nf"
@@ -331,7 +342,7 @@ build_info:
   output: "target/nextflow/workflows/htrnaseq"
   executable: "target/nextflow/workflows/htrnaseq/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf
index 3f94b36c..35c49f2a 100644
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3252,6 +3252,19 @@ meta = [
           "direction" : "output",
           "multiple" : false,
           "multiple_sep" : ";"
+        },
+        {
+          "type" : "file",
+          "name" : "--params",
+          "default" : [
+            "params.$id.yaml"
+          ],
+          "must_exist" : true,
+          "create_parent" : true,
+          "required" : true,
+          "direction" : "output",
+          "multiple" : false,
+          "multiple_sep" : ";"
         }
       ]
     }
@@ -3471,7 +3484,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
@@ -3543,14 +3556,6 @@ workflow run_wf {
         return [id, newState]
       }
 
-    // The featureData only has one requirement: the genome annotation.
-    // It can be generated straight away. Most of the time, there is one shared 
-    // annotation for all of the inputs and the fData should only be calculated once.
-    // The state is manpulated in such a way that there is one event created per unique
-    // input annotation file. In turn, the featureData file can joined into the original input
-    // channel which allows it to be shared across events if required.
-    f_data_ch = input_ch
-
       | save_params.run(
         fromState: {id, state ->
           // Define the function before using it
@@ -3558,8 +3563,10 @@ workflow run_wf {
           convertPaths = { value ->
             if (value instanceof java.nio.file.Path)
               return value.toUriString()
-            else if (value instanceof Collection)
+            else if (value instanceof List)
               return value.collect { convertPaths(it) }
+            else if (value instanceof Collection)
+              throw new UnsupportedOperationException("Collections other than Lists are not supported")
             else
               return value
           }
@@ -3574,12 +3581,21 @@ workflow run_wf {
           return [
             "id": id,
             "params_yaml": encodedYaml,
-            "output": "${id}_parameters.yaml"
+            "output": "params"
           ]
         },
-        toState: ["parameters": "output"]
+        toState: ["params": "output"]
       )
 
+    // The featureData only has one requirement: the genome annotation.
+    // It can be generated straight away. Most of the time, there is one shared 
+    // annotation for all of the inputs and the fData should only be calculated once.
+    // The state is manpulated in such a way that there is one event created per unique
+    // input annotation file. In turn, the featureData file can joined into the original input
+    // channel which allows it to be shared across events if required.
+    f_data_ch = input_ch
+
+
       | toSortedList()
       | flatMap {ids_and_states ->
         def annotation_files = ids_and_states.inject([:]){ old_state, id_and_state ->
@@ -3879,7 +3895,7 @@ workflow run_wf {
         "f_data": "f_data",
         "p_data": "p_data",
         "html_report": "html_report",
-        "parameters": "parameters",
+        "params": "params",
         "_meta": "_meta",
       ])
 
diff --git a/target/nextflow/workflows/htrnaseq/nextflow_schema.json b/target/nextflow/workflows/htrnaseq/nextflow_schema.json
index a4910c74..bacb3203 100644
--- a/target/nextflow/workflows/htrnaseq/nextflow_schema.json
+++ b/target/nextflow/workflows/htrnaseq/nextflow_schema.json
@@ -182,6 +182,17 @@
             }
     
 
+        ,
+                "params": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.params.yaml`. ",
+                "help_text": "Type: `file`, required, default: `$id.$key.params.yaml`. "
+            ,
+                "default":"$id.$key.params.yaml"
+            }
+    
+
 }
 },
     
diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml
index f838fb9a..4be428aa 100644
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -221,7 +221,7 @@ build_info:
   output: "target/nextflow/workflows/runner"
   executable: "target/nextflow/workflows/runner/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/utils/listInputDir"
diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf
index b2fb98a9..4a3531d0 100644
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3317,7 +3317,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
index 53fd118d..61883770 100644
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
   output: "target/nextflow/workflows/well_demultiplex"
   executable: "target/nextflow/workflows/well_demultiplex/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf
index 6d53fbbf..a81d8d27 100644
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3319,7 +3319,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_demultiplex",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
index 2db079dd..bfb61d61 100644
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -212,7 +212,7 @@ build_info:
   output: "target/nextflow/workflows/well_metadata"
   executable: "target/nextflow/workflows/well_metadata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a"
+  git_commit: "24e6d49c099294ef0cedbe2666fdf64e21aad0df"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf
index 24f5764b..0de44175 100644
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3299,7 +3299,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_metadata",
     "viash_version" : "0.9.2",
-    "git_commit" : "05ac6a3d2432d2da9a410388f33c45a78fd0cb1a",
+    "git_commit" : "24e6d49c099294ef0cedbe2666fdf64e21aad0df",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {