Build branch update-readme with version update-readme (fb376b1)

Build pipeline: viash-hub.htrnaseq.update-readme-wf7cg Source commit: fb376b1712 Source message: Experiment wit size of figure
2025-05-02 18:02:28 +00:00
parent b43c6ee280
commit 475d18a6a9
64 changed files with 163 additions and 135 deletions
--- 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

--- 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

--- 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
--- a/assets/launch-parameters-5-small.png
+++ b/assets/launch-parameters-5-small.png
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {
--- 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\
--- 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" : [
        {