Build branch v0.7 with version v0.7.1 (28baa17)

Build pipeline: viash-hub.htrnaseq.v0.7-gvsx6

Source commit: 28baa17391

Source message: Bump version to v0.7.1

CHANGELOG.md

@@ -1,3 +1,16 @@
+# 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).
+
+* `reporting`: updated default colour mapping (PR #50).
+
+## Minor changes
+
+* `create_report`: bump bioconductor version to 3.21 in order to accommodate R version 4.5 (PR #52).
+
 # htrnaseq v0.7.0
 
 ## Breaking changes

_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.7.0
+version: v0.7.1
 description: |
   High-throughput pipeline [WIP]
 license: MIT
@@ -8,7 +8,7 @@ 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:

src/report/config.vsh.yaml

@@ -40,6 +40,10 @@ engines:
         packages:
           - procps
           - pandoc
+      - type: r
+        script:
+          - install.packages("BiocManager")
+          - BiocManager::install(version = "3.21", type = "source", checkBuilt = TRUE)
       - type: r
         bioc:
           - Biobase

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)
+}

target/executable/eset/create_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -175,7 +175,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -202,18 +202,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -222,7 +223,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/eset/create_eset/create_eset

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# create_eset v0.7.0
+# create_eset v0.7.1
 # 
-# 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.
 # 
@@ -456,10 +456,10 @@ 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="2025-03-27T12:26:39Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_eset v0.7.0"
+  echo "create_eset v0.7.1"
   echo ""
   echo "Arguments:"
   echo "    --pDataFile"
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_eset v0.7.0"
+            echo "create_eset v0.7.1"
             exit
             ;;
         --pDataFile)
@@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.7.1'
   fi
 
   # print dockerfile

target/executable/eset/create_fdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -151,7 +151,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -179,18 +179,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -199,7 +200,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/eset/create_fdata/create_fdata

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# create_fdata v0.7.0
+# create_fdata v0.7.1
 # 
-# 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.
 # 
@@ -458,10 +458,10 @@ 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="2025-03-27T12:26:38Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_fdata v0.7.0"
+  echo "create_fdata v0.7.1"
   echo ""
   echo "Create a fdata file"
   echo ""
@@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_fdata v0.7.0"
+            echo "create_fdata v0.7.1"
             exit
             ;;
         --gtf)
@@ -756,7 +756,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.7.1'
   fi
 
   # print dockerfile

target/executable/eset/create_pdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -165,7 +165,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -193,18 +193,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -213,7 +214,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/eset/create_pdata/create_pdata

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# create_pdata v0.7.0
+# create_pdata v0.7.1
 # 
-# 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.
 # 
@@ -458,10 +458,10 @@ 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="2025-03-27T12:26:39Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pdata v0.7.0"
+  echo "create_pdata v0.7.1"
   echo ""
   echo "Create a pdata file by combining the mapping statistics"
   echo ""
@@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_pdata v0.7.0"
+            echo "create_pdata v0.7.1"
             exit
             ;;
         --star_stats_file)
@@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.7.1'
   fi
 
   # print dockerfile

target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -131,7 +131,7 @@ engines:
   id: "docker"
   image: "bioconductor/bioconductor_docker:3.19"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -151,18 +151,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -171,7 +172,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/integration_test_components/htrnaseq/check_eset/check_eset

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# check_eset v0.7.0
+# check_eset v0.7.1
 # 
-# 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.
 # 
@@ -455,10 +455,10 @@ 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="2025-03-27T12:26:38Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_eset v0.7.0"
+  echo "check_eset v0.7.1"
   echo ""
   echo "This component test the ExpressionSet object as output by the main pipeline."
   echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "check_eset v0.7.0"
+            echo "check_eset v0.7.1"
             exit
             ;;
         --eset)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.7.1'
   fi
 
   # print dockerfile

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -138,7 +138,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,18 +160,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -180,7 +181,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# check_cutadapt_output v0.7.0
+# check_cutadapt_output v0.7.1
 # 
-# 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.
 # 
@@ -457,10 +457,10 @@ 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="2025-03-27T12:26:39Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:50Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_cutadapt_output v0.7.0"
+  echo "check_cutadapt_output v0.7.1"
   echo ""
   echo "This component test the cutadapt output from the well_demultiplex subworkflow."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "check_cutadapt_output v0.7.0"
+            echo "check_cutadapt_output v0.7.1"
             exit
             ;;
         --fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.7.1'
   fi
 
   # print dockerfile

target/executable/io/publish_fastqs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.7.0"
+version: "v0.7.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -118,7 +118,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -135,18 +135,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -155,7 +156,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/publish_fastqs/publish_fastqs

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# publish_fastqs v0.7.0
+# publish_fastqs v0.7.1
 # 
-# 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.
 # 
@@ -450,10 +450,10 @@ 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="2025-03-27T12:26:38Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_fastqs v0.7.0"
+  echo "publish_fastqs v0.7.1"
   echo ""
   echo "Publish the fastq files per well"
   echo ""
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish_fastqs v0.7.0"
+            echo "publish_fastqs v0.7.1"
             exit
             ;;
         --input)
@@ -750,7 +750,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.7.1'
   fi
 
   # print dockerfile

target/executable/io/publish_results/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.7.0"
+version: "v0.7.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -172,7 +172,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -189,18 +189,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -209,7 +210,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/io/publish_results/publish_results

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# publish_results v0.7.0
+# publish_results v0.7.1
 # 
-# 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.
 # 
@@ -450,10 +450,10 @@ 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="2025-03-27T12:26:38Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_results v0.7.0"
+  echo "publish_results v0.7.1"
   echo ""
   echo "Publish the results"
   echo ""
@@ -649,7 +649,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish_results v0.7.0"
+            echo "publish_results v0.7.1"
             exit
             ;;
         --star_output)
@@ -864,7 +864,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.7.1'
   fi
 
   # print dockerfile

target/executable/parallel_map/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -245,7 +245,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -281,18 +281,19 @@ build_info:
   engine: "docker|native"
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
-  viash_version: "0.9.2"
-  git_commit: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -301,7 +302,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/parallel_map/parallel_map

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# parallel_map v0.7.0
+# parallel_map v0.7.1
 # 
-# 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.
 # 
@@ -461,10 +461,10 @@ 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="2025-03-27T12:26:39Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "parallel_map v0.7.0"
+  echo "parallel_map v0.7.1"
   echo ""
   echo "Map wells in batch, using STAR"
   echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "parallel_map v0.7.0"
+            echo "parallel_map v0.7.1"
             exit
             ;;
         --input_r1)
@@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.7.1'
   fi
 
   # print dockerfile

target/executable/report/create_report/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -156,7 +156,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,6 +164,12 @@ engines:
     - "procps"
     - "pandoc"
     interactive: false
+  - type: "r"
+    script:
+    - "install.packages(\"BiocManager\")"
+    - "BiocManager::install(version = \"3.21\", type = \"source\", checkBuilt = TRUE)"
+    bioc_force_install: false
+    warnings_as_errors: true
   - type: "r"
     cran:
     - "ggplot2"
@@ -205,18 +211,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -225,7 +232,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/report/create_report/create_report

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# create_report v0.7.0
+# create_report v0.7.1
 # 
-# 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.
 # 
@@ -453,6 +453,9 @@ RUN apt-get update && \
   DEBIAN_FRONTEND=noninteractive apt-get install -y procps pandoc && \
   rm -rf /var/lib/apt/lists/*
 
+RUN Rscript -e 'options(warn = 2); install.packages("BiocManager")' && \
+  Rscript -e 'options(warn = 2); BiocManager::install(version = "3.21", type = "source", checkBuilt = TRUE)'
+
 RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
   Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
   Rscript -e 'options(warn = 2); if (!requireNamespace("Biobase", quietly = TRUE)) BiocManager::install("Biobase")' && \
@@ -462,10 +465,10 @@ 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="2025-03-27T12:26:39Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:49Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -582,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_report v0.7.0"
+  echo "create_report v0.7.1"
   echo ""
   echo "Create a basic QC report in HTML format based on a number of esets."
   echo ""
@@ -641,7 +644,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_report v0.7.0"
+            echo "create_report v0.7.1"
             exit
             ;;
         --eset)
@@ -760,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.7.1'
   fi
 
   # print dockerfile

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)
+}

target/executable/stats/combine_star_logs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -172,7 +172,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -200,18 +200,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -220,7 +221,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/stats/combine_star_logs/combine_star_logs

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# combine_star_logs v0.7.0
+# combine_star_logs v0.7.1
 # 
-# 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.
 # 
@@ -457,10 +457,10 @@ 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="2025-03-27T12:26:37Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "combine_star_logs v0.7.0"
+  echo "combine_star_logs v0.7.1"
   echo ""
   echo "Arguments:"
   echo "    --barcodes"
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "combine_star_logs v0.7.0"
+            echo "combine_star_logs v0.7.1"
             exit
             ;;
         --barcodes)
@@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.7.1'
   fi
 
   # print dockerfile

target/executable/stats/generate_pool_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -156,7 +156,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -184,18 +184,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -204,7 +205,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/stats/generate_pool_statistics/generate_pool_statistics

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# generate_pool_statistics v0.7.0
+# generate_pool_statistics v0.7.1
 # 
-# 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.
 # 
@@ -458,10 +458,10 @@ 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="2025-03-27T12:26:38Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_pool_statistics v0.7.0"
+  echo "generate_pool_statistics v0.7.1"
   echo ""
   echo "Arguments:"
   echo "    --nrReadsNrGenesPerChrom"
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "generate_pool_statistics v0.7.0"
+            echo "generate_pool_statistics v0.7.1"
             exit
             ;;
         --nrReadsNrGenesPerChrom)
@@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.7.1'
   fi
 
   # print dockerfile

target/executable/stats/generate_well_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -227,7 +227,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -266,18 +266,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -286,7 +287,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/executable/stats/generate_well_statistics/generate_well_statistics

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
-# generate_well_statistics v0.7.0
+# generate_well_statistics v0.7.1
 # 
-# 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.
 # 
@@ -461,10 +461,10 @@ 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="2025-03-27T12:26:38Z"
+LABEL org.opencontainers.image.created="2025-04-30T10:35:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="a5d357e1c0642fd516dbb53d7456093239aef13e"
-LABEL org.opencontainers.image.version="v0.7.0"
+LABEL org.opencontainers.image.revision="28baa173918e524f8e7d2e4c51a8bad6ada64803"
+LABEL org.opencontainers.image.version="v0.7.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_well_statistics v0.7.0"
+  echo "generate_well_statistics v0.7.1"
   echo ""
   echo "Generate summary statistics from BAM files generated by STAR solo."
   echo ""
@@ -685,7 +685,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "generate_well_statistics v0.7.0"
+            echo "generate_well_statistics v0.7.1"
             exit
             ;;
         --input)
@@ -864,7 +864,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.7.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.7.1'
   fi
 
   # print dockerfile

target/nextflow/eset/create_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -175,7 +175,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -202,18 +202,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -222,7 +223,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/eset/create_eset/main.nf

@@ -1,6 +1,6 @@
-// create_eset v0.7.0
+// create_eset v0.7.1
 // 
-// 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
@@ -3041,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_eset",
   "namespace" : "eset",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3271,7 +3266,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3308,13 +3303,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3324,14 +3320,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3358,7 +3354,7 @@ 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 +4152,7 @@ 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 +4166,27 @@ 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
@@ -4183,7 +4200,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_eset",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_eset/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_eset'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
 

target/nextflow/eset/create_eset/nextflow_schema.json

@@ -57,10 +57,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output.rds`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.output.rds`. "
+                "description": "Type: `file`, required, default: `eset.$id.rds`. ",
+                "help_text": "Type: `file`, required, default: `eset.$id.rds`. "
             ,
-                "default":"$id.$key.output.rds"
+                "default":"eset.$id.rds"
             }
     
 

target/nextflow/eset/create_fdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -151,7 +151,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -179,18 +179,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -199,7 +200,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/eset/create_fdata/main.nf

@@ -1,6 +1,6 @@
-// create_fdata v0.7.0
+// create_fdata v0.7.1
 // 
-// 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
@@ -3041,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_fdata",
   "namespace" : "eset",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3238,7 +3233,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3278,13 +3273,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3294,14 +3290,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3328,7 +3324,7 @@ 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 +3817,7 @@ 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 +3831,27 @@ 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
@@ -3848,7 +3865,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_fdata",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_fdata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_fdata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Create a fdata file\n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/eset/create_fdata/nextflow_schema.json

@@ -27,10 +27,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.txt`. Tab-delimited text file containing information about the \u0027gene\u0027 or \u0027transcript\u0027\nentries from the input GTF file",
-                "help_text": "Type: `file`, default: `$id.$key.output.txt`. Tab-delimited text file containing information about the \u0027gene\u0027 or \u0027transcript\u0027\nentries from the input GTF file. The \u0027transcript\u0027 entries are used in case the source\nof the GTF was \u0027refGene\u0027 or \u0027ncbiRefSeq\u0027. \n"
+                "description": "Type: `file`, default: `fData.$id.txt`. Tab-delimited text file containing information about the \u0027gene\u0027 or \u0027transcript\u0027\nentries from the input GTF file",
+                "help_text": "Type: `file`, default: `fData.$id.txt`. Tab-delimited text file containing information about the \u0027gene\u0027 or \u0027transcript\u0027\nentries from the input GTF file. The \u0027transcript\u0027 entries are used in case the source\nof the GTF was \u0027refGene\u0027 or \u0027ncbiRefSeq\u0027. \n"
             ,
-                "default":"$id.$key.output.txt"
+                "default":"fData.$id.txt"
             }
     
 

target/nextflow/eset/create_pdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -165,7 +165,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -193,18 +193,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -213,7 +214,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/eset/create_pdata/main.nf

@@ -1,6 +1,6 @@
-// create_pdata v0.7.0
+// create_pdata v0.7.1
 // 
-// 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
@@ -3041,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_pdata",
   "namespace" : "eset",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3252,7 +3247,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3292,13 +3287,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3308,14 +3304,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3342,7 +3338,7 @@ 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 +3757,7 @@ 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 +3771,27 @@ 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
@@ -3788,7 +3805,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_pdata",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_pdata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_pdata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Create a pdata file by combining the mapping statistics \n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/eset/create_pdata/nextflow_schema.json

@@ -37,10 +37,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.txt`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output.txt`. "
+                "description": "Type: `file`, default: `pData.$id.txt`. ",
+                "help_text": "Type: `file`, default: `pData.$id.txt`. "
             ,
-                "default":"$id.$key.output.txt"
+                "default":"pData.$id.txt"
             }
     
 

target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -131,7 +131,7 @@ engines:
   id: "docker"
   image: "bioconductor/bioconductor_docker:3.19"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -151,18 +151,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -171,7 +172,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf

@@ -1,6 +1,6 @@
-// check_eset v0.7.0
+// check_eset v0.7.1
 // 
-// 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
@@ -3040,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "check_eset",
   "namespace" : "integration_test_components/htrnaseq",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3206,7 +3201,7 @@ meta = [
       "id" : "docker",
       "image" : "bioconductor/bioconductor_docker:3.19",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3232,13 +3227,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3248,14 +3244,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3282,7 +3278,7 @@ 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 +3851,7 @@ 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 +3865,27 @@ 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
@@ -3882,7 +3899,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'integration_test_components/htrnaseq/check_eset'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'This component test the ExpressionSet object as output by the main pipeline.'
   author = 'Dries Schaumont'
 }

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -138,7 +138,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -160,18 +160,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -180,7 +181,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf

@@ -1,6 +1,6 @@
-// check_cutadapt_output v0.7.0
+// check_cutadapt_output v0.7.1
 // 
-// 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
@@ -3040,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "check_cutadapt_output",
   "namespace" : "integration_test_components/well_demultiplexing",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3213,7 +3208,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3243,13 +3238,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3259,14 +3255,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3293,7 +3289,7 @@ 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 +3731,7 @@ 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 +3745,27 @@ 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
@@ -3762,7 +3779,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'integration_test_components/well_demultiplexing/check_cutadapt_output'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'This component test the cutadapt output from the well_demultiplex subworkflow.'
   author = 'Dries Schaumont'
 }

target/nextflow/io/publish_fastqs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.7.0"
+version: "v0.7.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -118,7 +118,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -135,18 +135,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -155,7 +156,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/publish_fastqs/main.nf

@@ -1,6 +1,6 @@
-// publish_fastqs v0.7.0
+// publish_fastqs v0.7.1
 // 
-// 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
@@ -3037,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish_fastqs",
   "namespace" : "io",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3184,7 +3179,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3206,13 +3201,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3222,14 +3218,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3631,7 +3627,7 @@ 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 +3641,27 @@ 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
@@ -3658,7 +3675,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/io/publish_fastqs",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish_fastqs/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish_fastqs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Publish the fastq files per well'
 }
 

target/nextflow/io/publish_fastqs/nextflow_schema.json

@@ -37,10 +37,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.output`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. "
+                "description": "Type: `file`, default: `$id`. ",
+                "help_text": "Type: `file`, default: `$id`. "
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id"
             }
     
 

target/nextflow/io/publish_results/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.7.0"
+version: "v0.7.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -172,7 +172,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -189,18 +189,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -209,7 +210,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/io/publish_results/main.nf

@@ -1,6 +1,6 @@
-// publish_results v0.7.0
+// publish_results v0.7.1
 // 
-// 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
@@ -3037,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish_results",
   "namespace" : "io",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3244,7 +3239,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3266,13 +3261,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3282,14 +3278,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3724,7 +3720,7 @@ 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 +3734,27 @@ 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
@@ -3751,7 +3768,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/io/publish_results",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish_results/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish_results'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Publish the results'
 }
 

target/nextflow/io/publish_results/nextflow_schema.json

@@ -97,10 +97,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.output`. ",
-                "help_text": "Type: `file`, default: `$id.$key.output.output`. "
+                "description": "Type: `file`, default: `$id`. ",
+                "help_text": "Type: `file`, default: `$id`. "
             ,
-                "default":"$id.$key.output.output"
+                "default":"$id"
             }
     
 

target/nextflow/parallel_map/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -245,7 +245,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -281,18 +281,19 @@ build_info:
   engine: "docker|native"
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -301,7 +302,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/parallel_map/main.nf

@@ -1,6 +1,6 @@
-// parallel_map v0.7.0
+// parallel_map v0.7.1
 // 
-// 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
@@ -3040,7 +3035,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "parallel_map",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3332,7 +3327,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3378,13 +3373,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3394,14 +3390,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -4120,7 +4116,7 @@ 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 +4130,27 @@ 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
@@ -4147,7 +4164,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/parallel_map",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/parallel_map/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'parallel_map'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n'
   author = 'Dries Schaumont, Toni Verbeiren'
 }

target/nextflow/parallel_map/nextflow_schema.json

@@ -119,10 +119,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\";\"`. A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.output_*./*`, multiple_sep: `\";\"`. A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome.\nThe order of the items DO NOT match with the order of the entries in the barcodes FASTA file or the input FASTQ pairs. \n"
+                "description": "Type: List of `file`, required, default: `./*`, multiple_sep: `\";\"`. A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome",
+                "help_text": "Type: List of `file`, required, default: `./*`, multiple_sep: `\";\"`. A list of output folders which are the result of using STAR to map each input FASTQ pair STAR to the reference genome.\nThe order of the items DO NOT match with the order of the entries in the barcodes FASTA file or the input FASTQ pairs. \n"
             ,
-                "default":"$id.$key.output_*./*"
+                "default":"./*"
             }
     
 
@@ -130,10 +130,10 @@
                 "joblog": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs",
-                "help_text": "Type: `file`, default: `$id.$key.joblog.txt`. Where to store the log file listing all the jobs."
+                "description": "Type: `file`, default: `execution_log.txt`. Where to store the log file listing all the jobs",
+                "help_text": "Type: `file`, default: `execution_log.txt`. Where to store the log file listing all the jobs."
             ,
-                "default":"$id.$key.joblog.txt"
+                "default":"execution_log.txt"
             }
     
 

target/nextflow/report/create_report/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -156,7 +156,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,6 +164,12 @@ engines:
     - "procps"
     - "pandoc"
     interactive: false
+  - type: "r"
+    script:
+    - "install.packages(\"BiocManager\")"
+    - "BiocManager::install(version = \"3.21\", type = \"source\", checkBuilt = TRUE)"
+    bioc_force_install: false
+    warnings_as_errors: true
   - type: "r"
     cran:
     - "ggplot2"
@@ -205,18 +211,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -225,7 +232,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/report/create_report/main.nf

@@ -1,6 +1,6 @@
-// create_report v0.7.0
+// create_report v0.7.1
 // 
-// 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
@@ -3041,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_report",
   "namespace" : "report",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3251,7 +3246,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3262,6 +3257,15 @@ meta = [
           ],
           "interactive" : false
         },
+        {
+          "type" : "r",
+          "script" : [
+            "install.packages(\\"BiocManager\\")",
+            "BiocManager::install(version = \\"3.21\\", type = \\"source\\", checkBuilt = TRUE)"
+          ],
+          "bioc_force_install" : false,
+          "warnings_as_errors" : true
+        },
         {
           "type" : "r",
           "cran" : [
@@ -3313,13 +3317,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3329,14 +3334,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3363,7 +3368,7 @@ 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.
@@ -3771,7 +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)
@@ -3785,6 +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
@@ -3798,7 +3824,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/report/create_report",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/report/create_report/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'report/create_report'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Create a basic QC report in HTML format based on a number of esets.\n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

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)
+}

target/nextflow/stats/combine_star_logs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -172,7 +172,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -200,18 +200,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -220,7 +221,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/stats/combine_star_logs/main.nf

@@ -1,6 +1,6 @@
-// combine_star_logs v0.7.0
+// combine_star_logs v0.7.1
 // 
-// 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
@@ -3040,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "combine_star_logs",
   "namespace" : "stats",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3254,7 +3249,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3294,13 +3289,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3310,14 +3306,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3344,7 +3340,7 @@ 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 +3922,7 @@ 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 +3936,27 @@ 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
@@ -3953,7 +3970,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/stats/combine_star_logs",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/stats/combine_star_logs/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'stats/combine_star_logs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   author = 'Dries Schaumont'
 }
 

target/nextflow/stats/combine_star_logs/nextflow_schema.json

@@ -57,10 +57,10 @@
                 "output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.output.txt`. Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)\ngathered from the different input files",
-                "help_text": "Type: `file`, default: `$id.$key.output.txt`. Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)\ngathered from the different input files. \n"
+                "description": "Type: `file`, default: `starLogs.txt`. Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)\ngathered from the different input files",
+                "help_text": "Type: `file`, default: `starLogs.txt`. Tab-delimited file describing for each barcode (as the rows), the metrics (as columns)\ngathered from the different input files. \n"
             ,
-                "default":"$id.$key.output.txt"
+                "default":"starLogs.txt"
             }
     
 

target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -156,7 +156,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -184,18 +184,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -204,7 +205,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/stats/generate_pool_statistics/main.nf

@@ -1,6 +1,6 @@
-// generate_pool_statistics v0.7.0
+// generate_pool_statistics v0.7.1
 // 
-// 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
@@ -3041,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "generate_pool_statistics",
   "namespace" : "stats",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3238,7 +3233,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3278,13 +3273,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3294,14 +3290,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3328,7 +3324,7 @@ 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 +3777,7 @@ 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 +3791,27 @@ 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
@@ -3808,7 +3825,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/stats/generate_pool_statistics",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/stats/generate_pool_statistics/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'stats/generate_pool_statistics'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
 

target/nextflow/stats/generate_well_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -227,7 +227,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.7.0"
+  target_tag: "v0.7.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -266,18 +266,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -286,7 +287,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/stats/generate_well_statistics/main.nf

@@ -1,6 +1,6 @@
-// generate_well_statistics v0.7.0
+// generate_well_statistics v0.7.1
 // 
-// 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
@@ -3041,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "generate_well_statistics",
   "namespace" : "stats",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3319,7 +3314,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.7.0",
+      "target_tag" : "v0.7.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3373,13 +3368,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3389,14 +3385,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3423,7 +3419,7 @@ 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 +3863,7 @@ 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 +3877,27 @@ 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
@@ -3894,7 +3911,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/stats/generate_well_statistics",
-    "tag" : "v0.7.0"
+    "tag" : "v0.7.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/stats/generate_well_statistics/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'stats/generate_well_statistics'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Generate summary statistics from BAM files generated by STAR solo.'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/stats/generate_well_statistics/nextflow_schema.json

@@ -47,10 +47,10 @@
                 "processedBAMFile": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.processedBAMFile.txt`. Path to a ",
-                "help_text": "Type: `file`, default: `$id.$key.processedBAMFile.txt`. Path to a .tsv file listing, per read in the BAM file,\nthe value for the \"CB\", \"UX\", \"GX\" and \"GN\" tag, together with the\nchromsome to which the read was mapped to.\n"
+                "description": "Type: `file`, default: `processedBamFile.txt`. Path to a ",
+                "help_text": "Type: `file`, default: `processedBamFile.txt`. Path to a .tsv file listing, per read in the BAM file,\nthe value for the \"CB\", \"UX\", \"GX\" and \"GN\" tag, together with the\nchromsome to which the read was mapped to.\n"
             ,
-                "default":"$id.$key.processedBAMFile.txt"
+                "default":"processedBamFile.txt"
             }
     
 
@@ -58,10 +58,10 @@
                 "nrReadsNrGenesPerChrom": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.nrReadsNrGenesPerChrom.txt`. Path to an output file that contains a ",
-                "help_text": "Type: `file`, default: `$id.$key.nrReadsNrGenesPerChrom.txt`. Path to an output file that contains a .tsv formatted table describing\nper chromosome the number of reads that were mapped to that chromosome (NumberOfReads\ncolumn) and the number of genes on that chromosome that had at least one\nread mapped to it (NumberOfGenes).\n"
+                "description": "Type: `file`, default: `nrReadsNrGenesPerChrom.txt`. Path to an output file that contains a ",
+                "help_text": "Type: `file`, default: `nrReadsNrGenesPerChrom.txt`. Path to an output file that contains a .tsv formatted table describing\nper chromosome the number of reads that were mapped to that chromosome (NumberOfReads\ncolumn) and the number of genes on that chromosome that had at least one\nread mapped to it (NumberOfGenes).\n"
             ,
-                "default":"$id.$key.nrReadsNrGenesPerChrom.txt"
+                "default":"nrReadsNrGenesPerChrom.txt"
             }
     
 
@@ -69,10 +69,10 @@
                 "nrReadsNrUMIsPerCB": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.nrReadsNrUMIsPerCB.txt`. Path to an output file that contains a ",
-                "help_text": "Type: `file`, default: `$id.$key.nrReadsNrUMIsPerCB.txt`. Path to an output file that contains a .tsv formatted table describing\nper barcode the number of UMI\u0027s (nrUMIs) and the total number of reads (NumberOfReads).\n"
+                "description": "Type: `file`, default: `nrReadsNrUMIsPerCB.txt`. Path to an output file that contains a ",
+                "help_text": "Type: `file`, default: `nrReadsNrUMIsPerCB.txt`. Path to an output file that contains a .tsv formatted table describing\nper barcode the number of UMI\u0027s (nrUMIs) and the total number of reads (NumberOfReads).\n"
             ,
-                "default":"$id.$key.nrReadsNrUMIsPerCB.txt"
+                "default":"nrReadsNrUMIsPerCB.txt"
             }
     
 
@@ -80,10 +80,10 @@
                 "umiFreqTop": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.umiFreqTop.txt`. Path to an output file that contains a ",
-                "help_text": "Type: `file`, default: `$id.$key.umiFreqTop.txt`. Path to an output file that contains a .tsv formatted table describing\nper UMI (column UB) the frequency at which they occur in the reads (column\nN). Only the top 100 UMIs are included.\n"
+                "description": "Type: `file`, default: `umiFreqTop100.txt`. Path to an output file that contains a ",
+                "help_text": "Type: `file`, default: `umiFreqTop100.txt`. Path to an output file that contains a .tsv formatted table describing\nper UMI (column UB) the frequency at which they occur in the reads (column\nN). Only the top 100 UMIs are included.\n"
             ,
-                "default":"$id.$key.umiFreqTop.txt"
+                "default":"umiFreqTop100.txt"
             }
     
 

target/nextflow/utils/concatRuns/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "concatRuns"
 namespace: "utils"
-version: "v0.7.0"
+version: "v0.7.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -156,20 +156,21 @@ build_info:
   engine: "native|native"
   output: "target/nextflow/utils/concatRuns"
   executable: "target/nextflow/utils/concatRuns/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
   dependencies:
   - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -178,7 +179,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/utils/concatRuns/main.nf

@@ -1,6 +1,6 @@
-// concatRuns v0.7.0
+// concatRuns v0.7.1
 // 
-// 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
@@ -3037,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "concatRuns",
   "namespace" : "utils",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3228,13 +3223,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3244,14 +3240,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/utils/concatRuns/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'utils/concatRuns'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Concatenate well FASTQ files from different runs in order to increase sequencing depth.\n'
 }
 

target/nextflow/utils/concatRuns/nextflow_schema.json

@@ -47,10 +47,10 @@
                 "output_r1": {
                 "type":
                 "string",
-                "description": "Type: List of `file`, default: `$id.$key.output_r1_*.output_r1_*`, multiple_sep: `\";\"`. Path to read 1 fastq/fasta file",
-                "help_text": "Type: List of `file`, default: `$id.$key.output_r1_*.output_r1_*`, multiple_sep: `\";\"`. Path to read 1 fastq/fasta file"
+                "description": "Type: List of `file`, default: `$id.$key.output_r1_*`, multiple_sep: `\";\"`. Path to read 1 fastq/fasta file",
+                "help_text": "Type: List of `file`, default: `$id.$key.output_r1_*`, multiple_sep: `\";\"`. Path to read 1 fastq/fasta file"
             ,
-                "default":"$id.$key.output_r1_*.output_r1_*"
+                "default":"$id.$key.output_r1_*"
             }
     
 
@@ -58,10 +58,10 @@
                 "output_r2": {
                 "type":
                 "string",
-                "description": "Type: List of `file`, default: `$id.$key.output_r2_*.output_r2_*`, multiple_sep: `\";\"`. Path to read 2 fastq/fasta file",
-                "help_text": "Type: List of `file`, default: `$id.$key.output_r2_*.output_r2_*`, multiple_sep: `\";\"`. Path to read 2 fastq/fasta file"
+                "description": "Type: List of `file`, default: `$id.$key.output_r2_*`, multiple_sep: `\";\"`. Path to read 2 fastq/fasta file",
+                "help_text": "Type: List of `file`, default: `$id.$key.output_r2_*`, multiple_sep: `\";\"`. Path to read 2 fastq/fasta file"
             ,
-                "default":"$id.$key.output_r2_*.output_r2_*"
+                "default":"$id.$key.output_r2_*"
             }
     
 

target/nextflow/utils/listInputDir/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "listInputDir"
 namespace: "utils"
-version: "v0.7.0"
+version: "v0.7.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -167,18 +167,19 @@ build_info:
   engine: "native|native"
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -187,7 +188,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/utils/listInputDir/main.nf

@@ -1,6 +1,6 @@
-// listInputDir v0.7.0
+// listInputDir v0.7.1
 // 
-// 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
@@ -3037,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "listInputDir",
   "namespace" : "utils",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3238,13 +3233,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3254,14 +3250,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/utils/listInputDir/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'utils/listInputDir'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'List the contents of a directory and parse contained fastq files'
 }
 

target/nextflow/utils/listInputDir/nextflow_schema.json

@@ -38,10 +38,10 @@
                 "r1_output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.r1_output.r1_output`. Path to read 1 fastq/fasta file",
-                "help_text": "Type: `file`, default: `$id.$key.r1_output.r1_output`. Path to read 1 fastq/fasta file"
+                "description": "Type: `file`, default: `$id.$key.r1_output`. Path to read 1 fastq/fasta file",
+                "help_text": "Type: `file`, default: `$id.$key.r1_output`. Path to read 1 fastq/fasta file"
             ,
-                "default":"$id.$key.r1_output.r1_output"
+                "default":"$id.$key.r1_output"
             }
     
 
@@ -49,10 +49,10 @@
                 "r2_output": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.r2_output.r2_output`. Path to read 2 fastq/fasta file",
-                "help_text": "Type: `file`, default: `$id.$key.r2_output.r2_output`. Path to read 2 fastq/fasta file"
+                "description": "Type: `file`, default: `$id.$key.r2_output`. Path to read 2 fastq/fasta file",
+                "help_text": "Type: `file`, default: `$id.$key.r2_output`. Path to read 2 fastq/fasta file"
             ,
-                "default":"$id.$key.r2_output.r2_output"
+                "default":"$id.$key.r2_output"
             }
     
 

target/nextflow/workflows/htrnaseq/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "htrnaseq"
 namespace: "workflows"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -327,9 +327,10 @@ build_info:
   engine: "native|native"
   output: "target/nextflow/workflows/htrnaseq"
   executable: "target/nextflow/workflows/htrnaseq/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
   - "target/nextflow/stats/generate_pool_statistics"
@@ -344,13 +345,13 @@ build_info:
   - "target/nextflow/utils/concatRuns"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -359,7 +360,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/workflows/htrnaseq/main.nf

@@ -1,6 +1,6 @@
-// htrnaseq v0.7.0
+// htrnaseq v0.7.1
 // 
-// 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
@@ -3040,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "htrnaseq",
   "namespace" : "workflows",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3464,13 +3459,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3480,14 +3476,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/workflows/htrnaseq/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/htrnaseq'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   author = 'Dries Schaumont'
 }
 

target/nextflow/workflows/htrnaseq/nextflow_schema.json

@@ -98,10 +98,10 @@
                 "fastq_output": {
                 "type":
                 "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.fastq_output_*.fastq_output_*`, multiple_sep: `\";\"`. Directory containing output fastq files",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.fastq_output_*.fastq_output_*`, multiple_sep: `\";\"`. Directory containing output fastq files"
+                "description": "Type: List of `file`, required, default: `fastq/*`, multiple_sep: `\";\"`. Directory containing output fastq files",
+                "help_text": "Type: List of `file`, required, default: `fastq/*`, multiple_sep: `\";\"`. Directory containing output fastq files"
             ,
-                "default":"$id.$key.fastq_output_*.fastq_output_*"
+                "default":"fastq/*"
             }
     
 
@@ -109,10 +109,10 @@
                 "star_output": {
                 "type":
                 "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.star_output_*.$id/*`, multiple_sep: `\";\"`. Output from mapping with STAR",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.star_output_*.$id/*`, multiple_sep: `\";\"`. Output from mapping with STAR"
+                "description": "Type: List of `file`, required, default: `star.$id/*`, multiple_sep: `\";\"`. Output from mapping with STAR",
+                "help_text": "Type: List of `file`, required, default: `star.$id/*`, multiple_sep: `\";\"`. Output from mapping with STAR"
             ,
-                "default":"$id.$key.star_output_*.$id/*"
+                "default":"star.$id/*"
             }
     
 
@@ -120,10 +120,10 @@
                 "nrReadsNrGenesPerChrom": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.nrReadsNrGenesPerChrom.txt`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.nrReadsNrGenesPerChrom.txt`. "
+                "description": "Type: `file`, required, default: `nrReadsNrGenesPerChrom.$id.txt`. ",
+                "help_text": "Type: `file`, required, default: `nrReadsNrGenesPerChrom.$id.txt`. "
             ,
-                "default":"$id.$key.nrReadsNrGenesPerChrom.txt"
+                "default":"nrReadsNrGenesPerChrom.$id.txt"
             }
     
 
@@ -131,10 +131,10 @@
                 "star_qc_metrics": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.star_qc_metrics.txt`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.star_qc_metrics.txt`. "
+                "description": "Type: `file`, required, default: `starLogs.$id.txt`. ",
+                "help_text": "Type: `file`, required, default: `starLogs.$id.txt`. "
             ,
-                "default":"$id.$key.star_qc_metrics.txt"
+                "default":"starLogs.$id.txt"
             }
     
 
@@ -142,10 +142,10 @@
                 "eset": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.eset.rds`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.eset.rds`. "
+                "description": "Type: `file`, required, default: `eset.$id.rds`. ",
+                "help_text": "Type: `file`, required, default: `eset.$id.rds`. "
             ,
-                "default":"$id.$key.eset.rds"
+                "default":"eset.$id.rds"
             }
     
 
@@ -153,10 +153,10 @@
                 "f_data": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.f_data.tsv`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.f_data.tsv`. "
+                "description": "Type: `file`, required, default: `fData.$id.tsv`. ",
+                "help_text": "Type: `file`, required, default: `fData.$id.tsv`. "
             ,
-                "default":"$id.$key.f_data.tsv"
+                "default":"fData.$id.tsv"
             }
     
 
@@ -164,10 +164,10 @@
                 "p_data": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.p_data.tsv`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.p_data.tsv`. "
+                "description": "Type: `file`, required, default: `pData.$id.tsv`. ",
+                "help_text": "Type: `file`, required, default: `pData.$id.tsv`. "
             ,
-                "default":"$id.$key.p_data.tsv"
+                "default":"pData.$id.tsv"
             }
     
 
@@ -175,10 +175,10 @@
                 "html_report": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.html_report.html`. ",
-                "help_text": "Type: `file`, required, default: `$id.$key.html_report.html`. "
+                "description": "Type: `file`, required, default: `report.$id.html`. ",
+                "help_text": "Type: `file`, required, default: `report.$id.html`. "
             ,
-                "default":"$id.$key.html_report.html"
+                "default":"report.$id.html"
             }
     
 

target/nextflow/workflows/runner/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "runner"
 namespace: "workflows"
-version: "v0.7.0"
+version: "v0.7.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -220,9 +220,10 @@ build_info:
   engine: "native|native"
   output: "target/nextflow/workflows/runner"
   executable: "target/nextflow/workflows/runner/main.nf"
-  viash_version: "0.9.2"
-  git_commit: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
   dependencies:
   - "target/nextflow/utils/listInputDir"
   - "target/nextflow/workflows/htrnaseq"
@@ -230,13 +231,13 @@ build_info:
   - "target/nextflow/io/publish_results"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -245,7 +246,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/workflows/runner/main.nf

@@ -1,6 +1,6 @@
-// runner v0.7.0
+// runner v0.7.1
 // 
-// 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
@@ -3037,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "runner",
   "namespace" : "workflows",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3316,13 +3311,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3332,14 +3328,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/workflows/runner/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/runner'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Runner for HT RNA-seq pipeline'
 }
 

target/nextflow/workflows/well_demultiplex/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "well_demultiplex"
 namespace: "workflows"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -213,21 +213,22 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
   - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -236,7 +237,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/workflows/well_demultiplex/main.nf

@@ -1,6 +1,6 @@
-// well_demultiplex v0.7.0
+// well_demultiplex v0.7.1
 // 
-// 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
@@ -3041,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "well_demultiplex",
   "namespace" : "workflows",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3318,13 +3313,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_demultiplex",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3334,14 +3330,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/workflows/well_demultiplex/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/well_demultiplex'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   description = 'Demultiplexing on well level'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/workflows/well_demultiplex/nextflow_schema.json

@@ -57,10 +57,10 @@
                 "output_r1": {
                 "type":
                 "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.output_r1_*.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.output_r1_*.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files"
+                "description": "Type: List of `file`, required, default: `fastq/*_R1_001.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files",
+                "help_text": "Type: List of `file`, required, default: `fastq/*_R1_001.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files"
             ,
-                "default":"$id.$key.output_r1_*.fastq"
+                "default":"fastq/*_R1_001.fastq"
             }
     
 
@@ -68,10 +68,10 @@
                 "output_r2": {
                 "type":
                 "string",
-                "description": "Type: List of `file`, required, default: `$id.$key.output_r2_*.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files",
-                "help_text": "Type: List of `file`, required, default: `$id.$key.output_r2_*.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files"
+                "description": "Type: List of `file`, required, default: `fastq/*_R2_001.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files",
+                "help_text": "Type: List of `file`, required, default: `fastq/*_R2_001.fastq`, multiple_sep: `\";\"`. List of demultiplexed fastq files"
             ,
-                "default":"$id.$key.output_r2_*.fastq"
+                "default":"fastq/*_R2_001.fastq"
             }
     
 

target/nextflow/workflows/well_metadata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "well_metadata"
 namespace: "workflows"
-version: "v0.7.0"
+version: "v0.7.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -211,18 +211,19 @@ 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: "a5d357e1c0642fd516dbb53d7456093239aef13e"
+  viash_version: "0.9.4"
+  git_commit: "28baa173918e524f8e7d2e4c51a8bad6ada64803"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.0-6-g28baa17"
 package_config:
   name: "htrnaseq"
-  version: "v0.7.0"
+  version: "v0.7.1"
   description: "High-throughput pipeline [WIP]\n"
   info:
     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:
@@ -231,7 +232,7 @@ package_config:
     \ dest: 'nextflow_labels.config'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
   keywords:
   - "bioinformatics"
   - "sequence"

target/nextflow/workflows/well_metadata/main.nf

@@ -1,6 +1,6 @@
-// well_metadata v0.7.0
+// well_metadata v0.7.1
 // 
-// 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
@@ -3040,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "well_metadata",
   "namespace" : "workflows",
-  "version" : "v0.7.0",
+  "version" : "v0.7.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3298,13 +3293,14 @@ meta = [
     "runner" : "nextflow",
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_metadata",
-    "viash_version" : "0.9.2",
-    "git_commit" : "a5d357e1c0642fd516dbb53d7456093239aef13e",
-    "git_remote" : "https://github.com/viash-hub/htrnaseq"
+    "viash_version" : "0.9.4",
+    "git_commit" : "28baa173918e524f8e7d2e4c51a8bad6ada64803",
+    "git_remote" : "https://github.com/viash-hub/htrnaseq",
+    "git_tag" : "v0.7.0-6-g28baa17"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.7.0",
+    "version" : "v0.7.1",
     "description" : "High-throughput pipeline [WIP]\n",
     "info" : {
       "test_resources" : [
@@ -3314,14 +3310,14 @@ meta = [
         }
       ]
     },
-    "viash_version" : "0.9.2",
+    "viash_version" : "0.9.4",
     "source" : "src",
     "target" : "target",
     "config_mods" : [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.7.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.7.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/workflows/well_metadata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'workflows/well_metadata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.7.0'
+  version = 'v0.7.1'
   author = 'Dries Schaumont'
 }
 

target/nextflow/workflows/well_metadata/nextflow_schema.json

@@ -67,10 +67,10 @@
                 "output_r1": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output_r1.output_r1`. Output fastq file",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_r1.output_r1`. Output fastq file."
+                "description": "Type: `file`, required, default: `$id.$key.output_r1`. Output fastq file",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_r1`. Output fastq file."
             ,
-                "default":"$id.$key.output_r1.output_r1"
+                "default":"$id.$key.output_r1"
             }
     
 
@@ -78,10 +78,10 @@
                 "output_r2": {
                 "type":
                 "string",
-                "description": "Type: `file`, required, default: `$id.$key.output_r2.output_r2`. Output fastq file",
-                "help_text": "Type: `file`, required, default: `$id.$key.output_r2.output_r2`. Output fastq file."
+                "description": "Type: `file`, required, default: `$id.$key.output_r2`. Output fastq file",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_r2`. Output fastq file."
             ,
-                "default":"$id.$key.output_r2.output_r2"
+                "default":"$id.$key.output_r2"
             }
     
 
@@ -129,10 +129,10 @@
                 "well_star_mapping": {
                 "type":
                 "string",
-                "description": "Type: `file`, default: `$id.$key.well_star_mapping.well_star_mapping`. ",
-                "help_text": "Type: `file`, default: `$id.$key.well_star_mapping.well_star_mapping`. "
+                "description": "Type: `file`, default: `$id.$key.well_star_mapping`. ",
+                "help_text": "Type: `file`, default: `$id.$key.well_star_mapping`. "
             ,
-                "default":"$id.$key.well_star_mapping.well_star_mapping"
+                "default":"$id.$key.well_star_mapping"
             }