diff --git a/README.md b/README.md
index 5e7d27dd..6a9a87cb 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,7 @@ version](https://img.shields.io/badge/Viash-v0.9.2-blue)](https://viash.io)
 ## Introduction
 
 This workflow is designed to process high-throughput RNA-seq data, where
-every well in a microarray plate is a sample. A fasta file provided as
+every well of a microarray plate is a sample. A fasta file provided as
 input defines the mapping between sample barcodes and wells.
 
 The workflow is built in a modular fashion, where most of the base
@@ -23,7 +23,8 @@ functionality is provided by components from
 supplemented by custom base components and workflow components in this
 package.
 
-The full workflow can be split in two major subworkflows:
+The full workflow is split in two major subworkflows that can be run
+independently:
 
 - **Well-demultiplexing:** Split the input (plate/pool level) fastq
   files per well.
@@ -41,6 +42,10 @@ run in two ways:
     where a number of choices (input/output structure and location) have
     been made.
 
+Input for the workflow has to be `fastq` files (zipped or not). For bcl
+or other formats, please consider running
+[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.
+
 ## Example usage
 
 ## Test and example data
@@ -68,10 +73,10 @@ Press the ‘Launch’ button and follow the instructions.
 ![](assets/htrnaseq-launch-small.png)
 
 We will start an example run loading just one input and using a barcodes
-fast file containing only 2 wells.
+fasta file containing only 2 wells.
 
 In the first step, we add the `local` profile to the list of profiles in
-order to the cpu and memory requirements of the workflow steps:
+order to limit the cpu and memory requirements of the workflow steps:
 
 ![](assets/launch-parameters-1-small.png) In the next step, we provide
 the paramters as follows:
@@ -87,7 +92,7 @@ the paramters as follows:
 - `annotation`:
   `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.annotation.gtf.gz`
 
-Please not the following: Both `input_r1` and `input_r2` take multiple
+Please note that both `input_r1` and `input_r2` can take multiple
 values. This means that one has to press ENTER after pasting the input
 path.
 
@@ -98,10 +103,11 @@ run the workflow from the CLI.
 
 ## Run using NF-Tower / Seqera Cloud
 
-It’s possible to run the workflow directly from Seqera Cloud. The
-necessary schema file has been built and provided with the workflows in
-order to use the form-based input. However, Seqera Cloud can not deal
-with multiple-value parameters when using the form -based input.
+It’s possible to run the workflow directly from [Seqera
+Cloud](https://cloud.seqera.io). The necessary schema file has been
+built and provided with the workflows in order to use the form-based
+input. However, Seqera Cloud can not deal with multiple-value parameters
+when using the form -based input.
 
 It’s better to use Viash Hub also here:
 
@@ -121,7 +127,18 @@ In the next screen, pressing the ‘Launch’ button will actually start the
 workflow on Seqera Cloud. A message is shown when the submit was
 successful.
 
-![](assets/launch-parameters-5-small.png)
+![](assets/launch-parameters-5-small.png) \## Run from the CLI
+
+Running from the CLI directly without using Viash hub is possible. The
+easiest is to just use the integrated help functionality, for instance
+using the following:
+
+``` bash
+ nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \
+  -revision v0.3.0 \
+  -main-script target/nextflow/workflows/runner/main.nf \
+  --help
+```
 
 # Contributions
 
diff --git a/README.qmd b/README.qmd
index be4ab77f..65a7730b 100644
--- a/README.qmd
+++ b/README.qmd
@@ -39,9 +39,9 @@ Open [Viash Hub](https://www.viash-hub.com) and browse to the [htrnaseq componen
 
 ![](assets/htrnaseq-launch-small.png)
 
-We will start an example run loading just one input and using a barcodes fast file containing only 2 wells.
+We will start an example run loading just one input and using a barcodes fasta file containing only 2 wells.
 
-In the first step, we add the `local` profile to the list of profiles in order to the cpu and memory requirements of the workflow steps:
+In the first step, we add the `local` profile to the list of profiles in order to limit the cpu and memory requirements of the workflow steps:
 
 
 ![](assets/launch-parameters-1-small.png)
@@ -53,7 +53,7 @@ In the next step, we provide the paramters as follows:
 - `barcodesFasta`: `gs://viash-hub-test-data/htrnaseq/v1/2-wells-with-ids.fasta`
 - `annotation`: `gs://viash-hub-test-data/htrnaseq/v1/genomeDir/gencode.v41.annotation.gtf.gz`
 
-Please not the following: Both `input_r1` and `input_r2` take multiple values. This means that one has to press ENTER after pasting the input path.
+Please note that both `input_r1` and `input_r2` can take multiple values. This means that one has to press ENTER after pasting the input path.
 
 ![](assets/launch-parameters-2-small.png)
 
@@ -62,7 +62,7 @@ Press the 'Launch' button at the end to get the instructions on how to run the w
 
 ## Run using NF-Tower / Seqera Cloud
 
-It's possible to run the workflow directly from Seqera Cloud. The necessary schema file has been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters when using  the form -based input.
+It's possible to run the workflow directly from [Seqera Cloud](https://cloud.seqera.io). The necessary schema file has been built and provided with the workflows in order to use the form-based input. However, Seqera Cloud can not deal with multiple-value parameters when using  the form -based input.
 
 It's better to use Viash Hub also here:
 
@@ -77,6 +77,17 @@ Next, we need to fill in the paramters for the run. This is similar to before:
 In the next screen, pressing the 'Launch' button will actually start the workflow on Seqera Cloud. A message is shown when the submit was successful.
 
 ![](assets/launch-parameters-5-small.png)
+## Run from the CLI
+
+Running from the CLI directly without using Viash hub is possible. The easiest is to just use the integrated help functionality, for instance using the following:
+
+```bash
+ nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \
+  -revision v0.3.0 \
+  -main-script target/nextflow/workflows/runner/main.nf \
+  --help
+```
+
 
 # Contributions
 
diff --git a/_viash.yaml b/_viash.yaml
index 59e641cd..e4d09436 100644
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -3,7 +3,7 @@ summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: |
   This workflow is designed to process high-throughput RNA-seq data, where every
-  well in a microarray plate is a sample. A fasta file provided as input
+  well of a microarray plate is a sample. A fasta file provided as input
   defines the mapping between sample barcodes and wells.
 
   The workflow is built in a modular fashion, where most of the base functionality
diff --git a/assets/launch-parameters-5-small.png b/assets/launch-parameters-5-small.png
index ddfc304c..53e36f43 100644
Binary files a/assets/launch-parameters-5-small.png and b/assets/launch-parameters-5-small.png differ
diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml
index 4ba3a778..9949e68c 100644
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -203,14 +203,14 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset
index bf0e1a8d..bf1a8a10 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="2025-05-02T16:11:19Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml
index 9744de80..a11c7529 100644
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -180,14 +180,14 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata
index 126b79cf..34a0f724 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="2025-05-02T16:11:19Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml
index 2117a39c..b01c745b 100644
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -194,14 +194,14 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata
index 74674914..5cad61d9 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="2025-05-02T16:11:19Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 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 37970f67..791c4d6d 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
@@ -152,14 +152,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
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 eb3ceac5..102b25ed 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="2025-05-02T16:11:18Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 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 f352f590..7e586079 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
@@ -161,14 +161,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
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 1d583325..98b94a6d 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="2025-05-02T16:11:20Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:48Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml
index 6f69b3a5..825f9607 100644
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -136,14 +136,14 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs
index f9cd0b8c..24687e05 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="2025-05-02T16:11:18Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml
index 82c0db13..38beae56 100644
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -190,14 +190,14 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results
index 7f9999ef..5296a05e 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="2025-05-02T16:11:18Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml
index 49af62c8..7d1d2791 100644
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -282,14 +282,14 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map
index 8c5385d1..ea63e3a0 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="2025-05-02T16:11:19Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml
index 36a5e5bc..67811c4f 100644
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -206,14 +206,14 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report
index b921fa95..95a6862a 100755
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -462,9 +462,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-05-02T16:11:19Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:47Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml
index b878ae1d..0a369903 100644
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -201,14 +201,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs
index 23f46ec1..45309f2c 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="2025-05-02T16:11:18Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
index 7d34f254..869bb257 100644
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,14 +185,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
index f0da4bb0..4004763f 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="2025-05-02T16:11:18Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
index 0a167b47..1db91cc5 100644
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,14 +267,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics
index e1579f30..79bb0217 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="2025-05-02T16:11:18Z"
+LABEL org.opencontainers.image.created="2025-05-02T17:15:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+LABEL org.opencontainers.image.revision="fb376b17126d0ff90904cc426799d88782b8c68d"
 LABEL org.opencontainers.image.version="update-readme"
 
 VIASHDOCKER
diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml
index 13665407..6fda0590 100644
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -203,14 +203,14 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf
index 47b7ebce..e87b5a31 100644
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3309,14 +3309,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml
index 9fe3e01b..8f684c89 100644
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -180,14 +180,14 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf
index ab91818f..41b6d379 100644
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3279,14 +3279,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml
index 24c41a2a..e1ecafe8 100644
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -194,14 +194,14 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf
index 5202f4eb..549817ea 100644
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3293,14 +3293,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
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 dcd3ba13..ead8c047 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
@@ -152,14 +152,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
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 5fd9258e..3282de39 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -3233,14 +3233,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
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 2d040046..23a03202 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
@@ -161,14 +161,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
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 75fe110b..236148b3 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
@@ -3244,14 +3244,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
index 9a25d08d..21066fa8 100644
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -136,14 +136,14 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf
index 53a17079..8f3b0e37 100644
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -3207,14 +3207,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml
index db60f97d..4593f3a4 100644
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -190,14 +190,14 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf
index ac651387..bd8250ec 100644
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3267,14 +3267,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml
index a50d53af..357fd428 100644
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -282,14 +282,14 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf
index 35e302e8..30e1b124 100644
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3379,14 +3379,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml
index 954c6e16..e4c6f6fa 100644
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -206,14 +206,14 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf
index e2f31721..640e68dd 100644
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3314,14 +3314,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
index ffb1833e..d532e3c2 100644
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -201,14 +201,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf
index d8d486f1..0f331d51 100644
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3295,14 +3295,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
index d8093861..5a868146 100644
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,14 +185,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf
index 703cabbf..efa1acc5 100644
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3279,14 +3279,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
index c9c90e46..2a7d2067 100644
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,14 +267,14 @@ 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf
index ac6420c1..4c7c2f19 100644
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3374,14 +3374,14 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml
index 954742b6..599f01f9 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
@@ -166,7 +166,7 @@ package_config:
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf
index 5f03b137..775002b6 100644
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,14 +3229,14 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml
index ca569c20..b9d72c5b 100644
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -168,14 +168,14 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf
index 720d820b..248af017 100644
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3239,14 +3239,14 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/listInputDir",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
index 766f2107..9b4aa78f 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
@@ -347,7 +347,7 @@ package_config:
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf
index df26d422..4ad69fd8 100644
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3465,14 +3465,14 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml
index d9874fa4..09c3559d 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/utils/listInputDir"
@@ -233,7 +233,7 @@ package_config:
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf
index a06b1a04..61b98be1 100644
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3317,14 +3317,14 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/runner",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
index b64f5788..a75c46f5 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: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
@@ -224,7 +224,7 @@ package_config:
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf
index 02fbfafa..00f528be 100644
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3319,14 +3319,14 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_demultiplex",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {
diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
index e41b72a8..283b2259 100644
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -212,14 +212,14 @@ build_info:
   output: "target/nextflow/workflows/well_metadata"
   executable: "target/nextflow/workflows/well_metadata/main.nf"
   viash_version: "0.9.2"
-  git_commit: "db4b3f68b2f5d18f357f4db6932d3186df28fd1c"
+  git_commit: "fb376b17126d0ff90904cc426799d88782b8c68d"
   git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "update-readme"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
-    \ where every\nwell in a microarray plate is a sample. A fasta file provided as\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
     \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
     \ is built in a modular fashion, where most of the base functionality\nis provided\
     \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf
index 506b9580..8d611971 100644
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3299,14 +3299,14 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_metadata",
     "viash_version" : "0.9.2",
-    "git_commit" : "db4b3f68b2f5d18f357f4db6932d3186df28fd1c",
+    "git_commit" : "fb376b17126d0ff90904cc426799d88782b8c68d",
     "git_remote" : "https://github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
     "version" : "update-readme",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
-    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell in a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
+    "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow can be split in two major subworkflows:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinianated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n",
     "info" : {
       "test_resources" : [
         {