Build branch main with version main (a948c26)

Build pipeline: viash-hub.htrnaseq.main-qpqxt Source commit: a948c26193 Source message: Bump viash to 0.9.4 (#51)
2025-04-29 13:35:02 +00:00
parent a95268a2b5
commit ccd3e04ddc
65 changed files with 1087 additions and 865 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,9 +1,18 @@
 # htrnaseq v0.7.1

+## Bug fixes
+
+* Bump viash version to `0.9.4`. This adds support for nextflow versions starting major version 25.01 and 
+fixes an issue where an integer being passed to a argument with `type: double` resulted in an error (PR #51).
+
 ## Minor changes

 * `create_report`: bump bioconductor version to 3.21 in order to accommodate R version 4.5 (PR #52).

+## Bug fixes
+
+* `reporting`: updated default colour mapping (PR #50).
+
 # htrnaseq v0.7.0

 ## Breaking changes
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -7,7 +7,7 @@ links:
  issue_tracker: https://github.com/viash-hub/htrnaseq/issues
  repository: https://github.com/viash-hub/htrnaseq

-viash_version: 0.9.2
+viash_version: 0.9.4

 info:
  test_resources:
--- a/src/report/plateLayouts.R
+++ b/src/report/plateLayouts.R
@@ -283,15 +283,31 @@ plateLayout <- function(

  if (is.null(colours)) {
    colours <- tryCatch({
-      colorRamp2(
+      circlize::colorRamp2(
        breaks = breaks,
        colors = brewer.pal(length(breaks), "Purples")
      )
    },
-    error = function(cond) {
-      return(c("#9370DB", "white"))
+    error = function(cond){
+      
+      message("Recomputed breaks for proper colour mapping")
+      
+      breakValues <- plateValues$values
+      breakValues[which(is.na(breakValues))] <- 0
+      if (all(breakValues >= 0)) {
+        breaks <- computeBreaks(7, max(plateValues$values, na.rm = TRUE))
+      } else {
+        breaks <- quantile(plateValues$values,  probs = seq(0, 1, 0.125))
+      }
+      
+      circlize::colorRamp2(
+        breaks = breaks,
+        colors = brewer.pal(length(breaks), "Purples")
+      )
+      
    })
  }
+  
  ht <- Heatmap(
    plateValues$values,
    column_title = mainTitle, column_title_side = "top",
@@ -425,6 +441,7 @@ computeBreaks <- function(nBreaks, variable) {
    )
    coefExp <- c(exp(coefSystem[1]), coefSystem[2])
    breaks <- coefExp[1] * exp((1:(nBreaks - 1)) * coefExp[2])
+    breaks <- unique(c(0, breaks))
  }
-  return(c(0, breaks))
-}
+  return(breaks)
+}
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -202,8 +202,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -213,7 +213,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -2,7 +2,7 @@

 # create_eset main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:40Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -179,8 +179,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -190,7 +190,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -2,7 +2,7 @@

 # create_fdata main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:40Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -193,8 +193,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -204,7 +204,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -2,7 +2,7 @@

 # create_pdata main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:41Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -151,8 +151,8 @@ build_info:
  engine: "docker|native"
  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: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -162,7 +162,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -2,7 +2,7 @@

 # check_eset main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:39Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- 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
@@ -160,8 +160,8 @@ build_info:
  engine: "docker|native"
  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: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -171,7 +171,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- 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
@@ -2,7 +2,7 @@

 # check_cutadapt_output main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:41Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -135,8 +135,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -146,7 +146,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -2,7 +2,7 @@

 # publish_fastqs main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:40Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -189,8 +189,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -200,7 +200,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -2,7 +2,7 @@

 # publish_results main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:40Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -281,8 +281,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -292,7 +292,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -2,7 +2,7 @@

 # parallel_map main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:41Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -211,8 +211,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -222,7 +222,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -2,7 +2,7 @@

 # create_report main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -465,9 +465,9 @@ 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="2025-04-29T11:22:41Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/report/create_report/plateLayouts.R
+++ b/target/executable/report/create_report/plateLayouts.R
@@ -283,15 +283,31 @@ plateLayout <- function(

  if (is.null(colours)) {
    colours <- tryCatch({
-      colorRamp2(
+      circlize::colorRamp2(
        breaks = breaks,
        colors = brewer.pal(length(breaks), "Purples")
      )
    },
-    error = function(cond) {
-      return(c("#9370DB", "white"))
+    error = function(cond){
+      
+      message("Recomputed breaks for proper colour mapping")
+      
+      breakValues <- plateValues$values
+      breakValues[which(is.na(breakValues))] <- 0
+      if (all(breakValues >= 0)) {
+        breaks <- computeBreaks(7, max(plateValues$values, na.rm = TRUE))
+      } else {
+        breaks <- quantile(plateValues$values,  probs = seq(0, 1, 0.125))
+      }
+      
+      circlize::colorRamp2(
+        breaks = breaks,
+        colors = brewer.pal(length(breaks), "Purples")
+      )
+      
    })
  }
+  
  ht <- Heatmap(
    plateValues$values,
    column_title = mainTitle, column_title_side = "top",
@@ -425,6 +441,7 @@ computeBreaks <- function(nBreaks, variable) {
    )
    coefExp <- c(exp(coefSystem[1]), coefSystem[2])
    breaks <- coefExp[1] * exp((1:(nBreaks - 1)) * coefExp[2])
+    breaks <- unique(c(0, breaks))
  }
-  return(c(0, breaks))
-}
+  return(breaks)
+}
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -200,8 +200,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -211,7 +211,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -2,7 +2,7 @@

 # combine_star_logs main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:39Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:55Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -184,8 +184,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -195,7 +195,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -2,7 +2,7 @@

 # generate_pool_statistics main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:40Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -266,8 +266,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -277,7 +277,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -2,7 +2,7 @@

 # generate_well_statistics main
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -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="2025-04-29T11:22:39Z"
+LABEL org.opencontainers.image.created="2025-04-29T12:46:56Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
+LABEL org.opencontainers.image.revision="a948c261931dbb784fc9ce6f7d5d93f52008a99f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -202,8 +202,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -213,7 +213,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -1,6 +1,6 @@
 // create_eset main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3308,8 +3303,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3324,7 +3319,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3358,7 +3353,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.R"
 cat > "$tempscript" << VIASHMAIN
 library(Biobase)
 library(data.table)
@@ -4156,7 +4151,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -4170,6 +4165,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -179,8 +179,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -190,7 +190,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -1,6 +1,6 @@
 // create_fdata main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3278,8 +3273,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3294,7 +3289,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3328,7 +3323,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import logging
 import pandas as pd
@@ -3821,7 +3816,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3835,6 +3830,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -193,8 +193,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -204,7 +204,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -1,6 +1,6 @@
 // create_pdata main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3292,8 +3287,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3308,7 +3303,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3342,7 +3337,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 from itertools import batched
 import pandas as pd
@@ -3761,7 +3756,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3775,6 +3770,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -151,8 +151,8 @@ build_info:
  engine: "docker|native"
  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: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -162,7 +162,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -1,6 +1,6 @@
 // check_eset main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3232,8 +3227,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3248,7 +3243,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3282,7 +3277,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.R"
 cat > "$tempscript" << VIASHMAIN
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3855,7 +3850,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3869,6 +3864,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- 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
@@ -160,8 +160,8 @@ build_info:
  engine: "docker|native"
  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: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -171,7 +171,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- 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
@@ -1,6 +1,6 @@
 // check_cutadapt_output main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3243,8 +3238,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3259,7 +3254,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3293,7 +3288,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import dnaio
 from operator import itemgetter
@@ -3735,7 +3730,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3749,6 +3744,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -135,8 +135,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -146,7 +146,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -1,6 +1,6 @@
 // publish_fastqs main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3206,8 +3201,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3222,7 +3217,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3631,7 +3626,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3645,6 +3640,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -189,8 +189,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -200,7 +200,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -1,6 +1,6 @@
 // publish_results main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3266,8 +3261,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3282,7 +3277,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3724,7 +3719,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3738,6 +3733,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -281,8 +281,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -292,7 +292,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -1,6 +1,6 @@
 // parallel_map main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3378,8 +3373,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3394,7 +3389,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -4120,7 +4115,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -4134,6 +4129,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -211,8 +211,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -222,7 +222,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -1,6 +1,6 @@
 // create_report main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3322,8 +3317,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3338,7 +3333,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3372,7 +3367,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.R"
 cat > "$tempscript" << VIASHMAIN
 ## VIASH START
 # The following code has been auto-generated by Viash.
@@ -3780,7 +3775,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3794,6 +3789,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/report/create_report/plateLayouts.R
+++ b/target/nextflow/report/create_report/plateLayouts.R
@@ -283,15 +283,31 @@ plateLayout <- function(

  if (is.null(colours)) {
    colours <- tryCatch({
-      colorRamp2(
+      circlize::colorRamp2(
        breaks = breaks,
        colors = brewer.pal(length(breaks), "Purples")
      )
    },
-    error = function(cond) {
-      return(c("#9370DB", "white"))
+    error = function(cond){
+      
+      message("Recomputed breaks for proper colour mapping")
+      
+      breakValues <- plateValues$values
+      breakValues[which(is.na(breakValues))] <- 0
+      if (all(breakValues >= 0)) {
+        breaks <- computeBreaks(7, max(plateValues$values, na.rm = TRUE))
+      } else {
+        breaks <- quantile(plateValues$values,  probs = seq(0, 1, 0.125))
+      }
+      
+      circlize::colorRamp2(
+        breaks = breaks,
+        colors = brewer.pal(length(breaks), "Purples")
+      )
+      
    })
  }
+  
  ht <- Heatmap(
    plateValues$values,
    column_title = mainTitle, column_title_side = "top",
@@ -425,6 +441,7 @@ computeBreaks <- function(nBreaks, variable) {
    )
    coefExp <- c(exp(coefSystem[1]), coefSystem[2])
    breaks <- coefExp[1] * exp((1:(nBreaks - 1)) * coefExp[2])
+    breaks <- unique(c(0, breaks))
  }
-  return(c(0, breaks))
-}
+  return(breaks)
+}
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -200,8 +200,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -211,7 +211,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -1,6 +1,6 @@
 // combine_star_logs main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3294,8 +3289,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3310,7 +3305,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3344,7 +3339,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import logging
 import pandas as pd
@@ -3926,7 +3921,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3940,6 +3935,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -184,8 +184,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -195,7 +195,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -1,6 +1,6 @@
 // generate_pool_statistics main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3278,8 +3273,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3294,7 +3289,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3328,7 +3323,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import pandas as pd
 from pathlib import Path
@@ -3781,7 +3776,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3795,6 +3790,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -266,8 +266,8 @@ build_info:
  engine: "docker|native"
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -277,7 +277,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -1,6 +1,6 @@
 // generate_well_statistics main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3373,8 +3368,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3389,7 +3384,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
@@ -3423,7 +3418,7 @@ meta = [
 // inner workflow hook
 def innerWorkflowFactory(args) {
  def rawScript = '''set -e
-tempscript=".viash_script.sh"
+tempscript=".viash_script.py"
 cat > "$tempscript" << VIASHMAIN
 import pysam
 import pandas as pd
@@ -3867,7 +3862,7 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  // create process from temp file
  def binding = new nextflow.script.ScriptBinding([:])
  def session = nextflow.Nextflow.getSession()
-  def parser = new nextflow.script.ScriptParser(session)
+  def parser = _getScriptLoader(session)
    .setModule(true)
    .setBinding(binding)
  def moduleScript = parser.runScript(tempFile)
@@ -3881,6 +3876,27 @@ def _vdsl3ProcessFactory(Map workflowArgs, Map meta, String rawScript) {
  return scriptMeta.getProcess(procKey)
 }

+// use Reflection to get a ScriptParser / ScriptLoader
+//   <25.02.0-edge: new nextflow.script.ScriptParser(session)
+//   >=25.02.0-edge: nextflow.script.ScriptLoaderFactory.create(session)
+def _getScriptLoader(nextflow.Session session) {
+  // try using the old method
+  try {
+    Class<?> scriptParserClass = Class.forName('nextflow.script.ScriptParser')
+    return scriptParserClass.getDeclaredConstructor(nextflow.Session).newInstance(session)
+  } catch (ClassNotFoundException e) {
+    // else try with the new method
+    try {
+      Class<?> scriptLoaderFactoryClass = Class.forName('nextflow.script.ScriptLoaderFactory')
+      def createMethod = scriptLoaderFactoryClass.getDeclaredMethod('create', nextflow.Session)
+      return createMethod.invoke(null, session) // null because create is static
+    } catch (ClassNotFoundException | NoSuchMethodException | IllegalAccessException | java.lang.reflect.InvocationTargetException e2) {
+      // Handle the case where neither class is found
+      throw new Exception("Neither nextflow.script.ScriptParser nor nextflow.script.ScriptLoaderFactory could be found. Is this a compatible Nextflow version?", e2)
+    }
+  }
+}
+
 // defaults
 meta["defaults"] = [
  // key to be used to trace the process and determine output names
--- a/target/nextflow/utils/concatRuns/.config.vsh.yaml
+++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml
@@ -156,8 +156,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/utils/concatRuns"
  executable: "target/nextflow/utils/concatRuns/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
@@ -169,7 +169,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -1,6 +1,6 @@
 // concatRuns main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3228,8 +3223,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/utils/concatRuns",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3244,7 +3239,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -167,8 +167,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -178,7 +178,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -1,6 +1,6 @@
 // listInputDir main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3238,8 +3233,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3254,7 +3249,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -327,8 +327,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
@@ -350,7 +350,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -1,6 +1,6 @@
 // htrnaseq main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3464,8 +3459,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3480,7 +3475,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -220,8 +220,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/workflows/runner"
  executable: "target/nextflow/workflows/runner/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/utils/listInputDir"
@@ -236,7 +236,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -1,6 +1,6 @@
 // runner main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -82,64 +82,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -151,10 +143,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3316,8 +3311,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3332,7 +3327,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -213,8 +213,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
@@ -227,7 +227,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -1,6 +1,6 @@
 // well_demultiplex main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -86,64 +86,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -155,10 +147,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3318,8 +3313,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3334,7 +3329,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -211,8 +211,8 @@ build_info:
  engine: "native|native"
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
+  viash_version: "0.9.4"
+  git_commit: "a948c261931dbb784fc9ce6f7d5d93f52008a99f"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
@@ -222,7 +222,7 @@ package_config:
    test_resources:
    - path: "gs://viash-hub-test-data/htrnaseq/v1/"
      dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
  source: "src"
  target: "target"
  config_mods:
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -1,6 +1,6 @@
 // well_metadata main
 // 
-// This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+// This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 // Intuitive.
 // 
@@ -85,64 +85,56 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
      foundClass = "List[${e.foundClass}]"
    }
  } else if (par.type == "string") {
-    // cast to string if need be
+    // cast to string if need be. only cast if the value is a GString
    if (value instanceof GString) {
-      value = value.toString()
+      value = value as String
    }
    expectedClass = value instanceof String ? null : "String"
  } else if (par.type == "integer") {
    // cast to integer if need be
-    if (value instanceof String) {
+    if (value !instanceof Integer) {
      try {
-        value = value.toInteger()
+        value = value as Integer
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Integer"
      }
    }
-    if (value instanceof java.math.BigInteger) {
-      value = value.intValue()
-    }
-    expectedClass = value instanceof Integer ? null : "Integer"
  } else if (par.type == "long") {
    // cast to long if need be
-    if (value instanceof String) {
+    if (value !instanceof Long) {
      try {
-        value = value.toLong()
+        value = value as Long
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Long"
      }
    }
-    if (value instanceof Integer) {
-      value = value.toLong()
-    }
-    expectedClass = value instanceof Long ? null : "Long"
  } else if (par.type == "double") {
    // cast to double if need be
-    if (value instanceof String) {
+    if (value !instanceof Double) {
      try {
-        value = value.toDouble()
+        value = value as Double
      } catch (NumberFormatException e) {
-        // do nothing
+        expectedClass = "Double"
      }
    }
-    if (value instanceof java.math.BigDecimal) {
-      value = value.doubleValue()
+  } else if (par.type == "float") {
+    // cast to float if need be
+    if (value !instanceof Float) {
+      try {
+        value = value as Float
+      } catch (NumberFormatException e) {
+        expectedClass = "Float"
+      }
    }
-    if (value instanceof Float) {
-      value = value.toDouble()
-    }
-    expectedClass = value instanceof Double ? null : "Double"
  } else if (par.type == "boolean" | par.type == "boolean_true" | par.type == "boolean_false") {
    // cast to boolean if need be
-    if (value instanceof String) {
-      def valueLower = value.toLowerCase()
-      if (valueLower == "true") {
-        value = true
-      } else if (valueLower == "false") {
-        value = false
+    if (value !instanceof Boolean) {
+      try {
+        value = value as Boolean
+      } catch (Exception e) {
+        expectedClass = "Boolean"
      }
    }
-    expectedClass = value instanceof Boolean ? null : "Boolean"
  } else if (par.type == "file" && (par.direction == "input" || stage == "output")) {
    // cast to path if need be
    if (value instanceof String) {
@@ -154,10 +146,13 @@ def _checkArgumentType(String stage, Map par, Object value, String errorIdentifi
    expectedClass = value instanceof Path ? null : "Path"
  } else if (par.type == "file" && stage == "input" && par.direction == "output") {
    // cast to string if need be
-    if (value instanceof GString) {
-      value = value.toString()
+    if (value !instanceof String) {
+      try {
+        value = value as String
+      } catch (Exception e) {
+        expectedClass = "String"
+      }
    }
-    expectedClass = value instanceof String ? null : "String"
  } else {
    // didn't find a match for par.type
    expectedClass = par.type
@@ -3298,8 +3293,8 @@ meta = [
    "runner" : "nextflow",
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
-    "viash_version" : "0.9.2",
-    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
+    "viash_version" : "0.9.4",
+    "git_commit" : "a948c261931dbb784fc9ce6f7d5d93f52008a99f",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3314,7 +3309,7 @@ meta = [
        }
      ]
    },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
    "source" : "src",
    "target" : "target",
    "config_mods" : [