diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0003c64f..bc0b9720 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# htrnaseq v0.7.1
+
+## 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
diff --git a/src/report/config.vsh.yaml b/src/report/config.vsh.yaml
index cf0efbd7..c00ca403 100644
--- a/src/report/config.vsh.yaml
+++ b/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
diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml
index 1e47bbe6..21e0a6ae 100644
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -203,7 +203,7 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset
index 05f6c1fe..68b9d5c5 100755
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:07Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml
index 772457b1..83efd10d 100644
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -180,7 +180,7 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata
index e238f879..4f8f2a37 100755
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:06Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml
index 82e4d0e0..a74b8730 100644
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -194,7 +194,7 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata
index ea7a5f5f..b9649855 100755
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:07Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index e8db7b8b..35b647bd 100644
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -152,7 +152,7 @@ build_info:
   output: "target/executable/integration_test_components/htrnaseq/check_eset"
   executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
index 15ef06df..72529f3c 100755
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:06Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index 02375872..4d4b850d 100644
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -161,7 +161,7 @@ build_info:
   output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
index ea6c3d35..22467629 100755
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:07Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml
index a9922968..29a9e575 100644
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -136,7 +136,7 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs
index 125c4d45..6ec5a421 100755
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:06Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml
index 5c5ffec3..12edb9c3 100644
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results
index 9cc9f82e..e10cf7db 100755
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -450,9 +450,9 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:06Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml
index f6d62f8c..0762ec78 100644
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -282,7 +282,7 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map
index 4bf42e66..3ec9ecfe 100755
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:07Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml
index f24b73b8..176bcf73 100644
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -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"
@@ -206,7 +212,7 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report
index 8a7ad5f5..72f01dd8 100755
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -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")' && \
@@ -462,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:07Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:41Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml
index 32bc1e20..5d3073df 100644
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
   output: "target/executable/stats/combine_star_logs"
   executable: "target/executable/stats/combine_star_logs/combine_star_logs"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs
index 1aeed84e..1b288618 100755
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:05Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
index b446a121..948a3057 100644
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
   output: "target/executable/stats/generate_pool_statistics"
   executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
index da065b02..8b2cee0d 100755
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:06Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:40Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
index 94bdd254..6db009a8 100644
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,7 +267,7 @@ build_info:
   output: "target/executable/stats/generate_well_statistics"
   executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics
index b8697218..4e7a35cc 100755
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -461,9 +461,9 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-03-27T12:20:06Z"
+LABEL org.opencontainers.image.created="2025-04-29T11:22:39Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+LABEL org.opencontainers.image.revision="cb58990a33f6ea6e46e474f2095b10218cf08912"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml
index b1f73f8b..c93e16c5 100644
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -203,7 +203,7 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf
index b9eb49cc..fd36a37a 100644
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3309,7 +3309,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/eset/create_eset/nextflow_schema.json b/target/nextflow/eset/create_eset/nextflow_schema.json
index 1e6f217e..0dc57228 100644
--- a/target/nextflow/eset/create_eset/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml
index 6cafa28c..962ac9a8 100644
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -180,7 +180,7 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf
index f9cfa262..7f39fb70 100644
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3279,7 +3279,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/eset/create_fdata/nextflow_schema.json b/target/nextflow/eset/create_fdata/nextflow_schema.json
index cde29031..69cc44b1 100644
--- a/target/nextflow/eset/create_fdata/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml
index a96a3e45..cbe653e4 100644
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -194,7 +194,7 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf
index e25a0a1f..d444726d 100644
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3293,7 +3293,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/eset/create_pdata/nextflow_schema.json b/target/nextflow/eset/create_pdata/nextflow_schema.json
index e7a40906..85da40c1 100644
--- a/target/nextflow/eset/create_pdata/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 34c3e8db..9e66afff 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -152,7 +152,7 @@ build_info:
   output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
   executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
index 9d49e043..8405fc7e 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -3233,7 +3233,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
index d438dba8..3cc06c79 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -161,7 +161,7 @@ build_info:
   output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
index e62f9aae..571c2769 100644
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -3244,7 +3244,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
index f10f019c..ce2a26cf 100644
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -136,7 +136,7 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf
index 30392dba..d85fc9b1 100644
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -3207,7 +3207,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/io/publish_fastqs/nextflow_schema.json b/target/nextflow/io/publish_fastqs/nextflow_schema.json
index 1417eaf2..f341fc18 100644
--- a/target/nextflow/io/publish_fastqs/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml
index 2168d3c2..33206335 100644
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf
index beb35c1f..7d9836c1 100644
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3267,7 +3267,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/io/publish_results/nextflow_schema.json b/target/nextflow/io/publish_results/nextflow_schema.json
index 570c5e95..3e2af79f 100644
--- a/target/nextflow/io/publish_results/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml
index 911a11a3..45d076bb 100644
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -282,7 +282,7 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf
index 421f8495..6f5cb9ca 100644
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3379,7 +3379,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/parallel_map/nextflow_schema.json b/target/nextflow/parallel_map/nextflow_schema.json
index e87db781..ce9ea034 100644
--- a/target/nextflow/parallel_map/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml
index 4ef92986..b6bd0876 100644
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -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"
@@ -206,7 +212,7 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf
index cdb27ee4..902769da 100644
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3262,6 +3262,15 @@ 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" : [
@@ -3314,7 +3323,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
index db40cf15..36eb2d3a 100644
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
   output: "target/nextflow/stats/combine_star_logs"
   executable: "target/nextflow/stats/combine_star_logs/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf
index 9cea48d1..93d9df05 100644
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3295,7 +3295,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/combine_star_logs/nextflow_schema.json b/target/nextflow/stats/combine_star_logs/nextflow_schema.json
index 72f77d8b..d8ae39a9 100644
--- a/target/nextflow/stats/combine_star_logs/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
index 1b7dbf6d..f2580e87 100644
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
   output: "target/nextflow/stats/generate_pool_statistics"
   executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf
index 2ee15f39..6c72c0b8 100644
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3279,7 +3279,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
index 28a24569..f3c7e219 100644
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,7 +267,7 @@ build_info:
   output: "target/nextflow/stats/generate_well_statistics"
   executable: "target/nextflow/stats/generate_well_statistics/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf
index 5deb44ed..a5f0ecd8 100644
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3374,7 +3374,7 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/stats/generate_well_statistics/nextflow_schema.json b/target/nextflow/stats/generate_well_statistics/nextflow_schema.json
index 3e2b583d..a432968c 100644
--- a/target/nextflow/stats/generate_well_statistics/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml
index 33909e61..4680a64d 100644
--- a/target/nextflow/utils/concatRuns/.config.vsh.yaml
+++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml
@@ -157,7 +157,7 @@ build_info:
   output: "target/nextflow/utils/concatRuns"
   executable: "target/nextflow/utils/concatRuns/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf
index e5e3341a..83d4c6de 100644
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,7 +3229,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/concatRuns/nextflow_schema.json b/target/nextflow/utils/concatRuns/nextflow_schema.json
index 1a1fd221..e39d0478 100644
--- a/target/nextflow/utils/concatRuns/nextflow_schema.json
+++ b/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_*"
             }
     
 
diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml
index 12dcc401..da5fff4f 100644
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -168,7 +168,7 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf
index a2678eaa..29886c95 100644
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3239,7 +3239,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/utils/listInputDir/nextflow_schema.json b/target/nextflow/utils/listInputDir/nextflow_schema.json
index 0e90a1d0..ee2f29c9 100644
--- a/target/nextflow/utils/listInputDir/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
index e527b2a6..008ce54f 100644
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -328,7 +328,7 @@ build_info:
   output: "target/nextflow/workflows/htrnaseq"
   executable: "target/nextflow/workflows/htrnaseq/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf
index b58e5e2b..48c9f2bc 100644
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3465,7 +3465,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/htrnaseq/nextflow_schema.json b/target/nextflow/workflows/htrnaseq/nextflow_schema.json
index a4910c74..82dfb8cb 100644
--- a/target/nextflow/workflows/htrnaseq/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml
index 63790b9e..411a12cf 100644
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -221,7 +221,7 @@ build_info:
   output: "target/nextflow/workflows/runner"
   executable: "target/nextflow/workflows/runner/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/utils/listInputDir"
diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf
index 0b5d0307..9264ab9e 100644
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3317,7 +3317,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
index ed2adc43..4fa24c49 100644
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
   output: "target/nextflow/workflows/well_demultiplex"
   executable: "target/nextflow/workflows/well_demultiplex/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf
index 35a473d5..3d45d086 100644
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3319,7 +3319,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_demultiplex",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/well_demultiplex/nextflow_schema.json b/target/nextflow/workflows/well_demultiplex/nextflow_schema.json
index 8be4ff28..9b7209ac 100644
--- a/target/nextflow/workflows/well_demultiplex/nextflow_schema.json
+++ b/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"
             }
     
 
diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
index 5cc52d11..9a0ff5ed 100644
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -212,7 +212,7 @@ build_info:
   output: "target/nextflow/workflows/well_metadata"
   executable: "target/nextflow/workflows/well_metadata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "0cb29cf43ad6d7a669cc207040c72b7e164985f6"
+  git_commit: "cb58990a33f6ea6e46e474f2095b10218cf08912"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf
index cb5b8535..563874d7 100644
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3299,7 +3299,7 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_metadata",
     "viash_version" : "0.9.2",
-    "git_commit" : "0cb29cf43ad6d7a669cc207040c72b7e164985f6",
+    "git_commit" : "cb58990a33f6ea6e46e474f2095b10218cf08912",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
diff --git a/target/nextflow/workflows/well_metadata/nextflow_schema.json b/target/nextflow/workflows/well_metadata/nextflow_schema.json
index f2f2f1ba..5418332f 100644
--- a/target/nextflow/workflows/well_metadata/nextflow_schema.json
+++ b/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"
             }