Build branch main with version main (cb58990)

Build pipeline: viash-hub.htrnaseq.main-mjsqg Source commit: cb58990a33 Source message: Fix create_report build after R update (#52)
2025-04-29 12:11:45 +00:00
parent 82d0d471e5
commit a95268a2b5
75 changed files with 193 additions and 159 deletions
--- 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
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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
--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
--- 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" : {
--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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_*"
            }
    

--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
--- 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" : {
--- 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"
            }
    

--- 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"
--- 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" : {
--- 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"
            }