Build branch update-readme with version update-readme (9169713)

Build pipeline: viash-hub.htrnaseq.update-readme-rbqnh Source commit: 916971370f Source message: Fix mermaid diagram
2025-05-06 09:26:17 +00:00
parent e13b40221c
commit 0d034eda71
62 changed files with 112 additions and 88 deletions
--- a/README.md
+++ b/README.md
@@ -46,27 +46,49 @@ 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.

-\`\`\`mermaid lang=‘mermaid’ flowchart TB subgraph runner \[runner\]
-direction TB subgraph htrnaseq [HT-RNAseq](#ht-rnaseq) direction LR
-demultiplex \[“Well demultiplexing”\] map report eset end end
+``` mermaid lang="mermaid"
+flowchart TB
+  subgraph runner [runner]
+    direction TB
+    subgraph htrnaseq [HT-RNAseq]
+      direction LR
+      demultiplex[Well demultiplexing]
+      map
+      report
+      eset
+    end
+  end

-demultiplex –\> map –\> report –\> eset
+  demultiplex --> map --> report --> eset

-class runner container class htrnaseq container class demultiplex
-container-inner class map container-inner class report container-inner
-class eset container-inner
+  class runner container
+  class htrnaseq container
+  class demultiplex container-inner
+  class map container-inner
+  class report container-inner
+  class eset container-inner

-class demultiplex node class map node class report node class eset node
+  class demultiplex node
+  class map node
+  class report node
+  class eset node
+```

+## Example usage

-    ## Example usage
+### Test and example data

-    ### Test and example data
+If you want to explore this workflow, it’s possible to the use data we
+use as test data: [a DRUGseq
+dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176150)
+from the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra).
+For the unit and integration tests, this data has been (partly)
+subsampled to reduce the test runtime. We used
+[seqtk](https://github.com/lh3/seqtk) for this with a seed of 1, e.g.:

-    If you want to explore this workflow, it's possible to the use data we use as test data: [a DRUGseq dataset](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176150) from the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra). For the unit and integration tests, this data has been (partly) subsampled to reduce the test runtime. We used [seqtk](https://github.com/lh3/seqtk) for this with a seed of 1, e.g.:
-
-    ```bash
-    seqtk sample -s1 orig/SRR14730302/VH02001614_S8_R1_001.fastq.gz 10000 > 10k/SRR14730302/VH02001614_S8_R1_001.fastq.gz
+``` bash
+seqtk sample -s1 orig/SRR14730302/VH02001614_S8_R1_001.fastq.gz 10000 > 10k/SRR14730302/VH02001614_S8_R1_001.fastq.gz
+```

 This data is available at: `gs://viash-hub-test-data/htrnaseq/v1/`.

--- a/README.qmd
+++ b/README.qmd
@@ -20,13 +20,14 @@ contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")

 `r project$description`

-```mermaid lang='mermaid'
+
+```{mermaid lang='mermaid'}
 flowchart TB
  subgraph runner [runner]
    direction TB
    subgraph htrnaseq [HT-RNAseq]
      direction LR
-      demultiplex ["Well demultiplexing"]
+      demultiplex[Well demultiplexing]
      map
      report
      eset
@@ -48,6 +49,7 @@ flowchart TB
  class eset node
 ```

+
 ## Example usage

 ### Test and example data
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -203,7 +203,7 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:24Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -180,7 +180,7 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_fdata/create_fdata
+++ b/target/executable/eset/create_fdata/create_fdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:24Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -194,7 +194,7 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/eset/create_pdata/create_pdata
+++ b/target/executable/eset/create_pdata/create_pdata
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:24Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -152,7 +152,7 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
@@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:23Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -161,7 +161,7 @@ build_info:
  output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:25Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -136,7 +136,7 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/io/publish_fastqs/publish_fastqs
+++ b/target/executable/io/publish_fastqs/publish_fastqs
@@ -450,9 +450,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:24Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -190,7 +190,7 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/io/publish_results/publish_results
+++ b/target/executable/io/publish_results/publish_results
@@ -450,9 +450,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:24Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 LABEL org.opencontainers.image.version="update-readme"

 VIASHDOCKER
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -282,7 +282,7 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:25Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -206,7 +206,7 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -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="2025-05-06T06:28:25Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:46Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -201,7 +201,7 @@ build_info:
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/combine_star_logs/combine_star_logs
+++ b/target/executable/stats/combine_star_logs/combine_star_logs
@@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:23Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -185,7 +185,7 @@ build_info:
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics
+++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
@@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:24Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -267,7 +267,7 @@ build_info:
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/executable/stats/generate_well_statistics/generate_well_statistics
+++ b/target/executable/stats/generate_well_statistics/generate_well_statistics
@@ -461,9 +461,9 @@ RUN pip install --upgrade pip && \

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-05-06T06:28:23Z"
+LABEL org.opencontainers.image.created="2025-05-06T08:39:44Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="3516346356891d56d98673343f9e61ab0919199e"
+LABEL org.opencontainers.image.revision="916971370f30aeb2e30ccaa9291d37958a2b01d0"
 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
@@ -203,7 +203,7 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3309,7 +3309,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -180,7 +180,7 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3279,7 +3279,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -194,7 +194,7 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3293,7 +3293,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -152,7 +152,7 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -3233,7 +3233,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -161,7 +161,7 @@ build_info:
  output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
  executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
+++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf
@@ -3244,7 +3244,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -136,7 +136,7 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -3207,7 +3207,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3267,7 +3267,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -282,7 +282,7 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3379,7 +3379,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -206,7 +206,7 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3314,7 +3314,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -201,7 +201,7 @@ build_info:
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3295,7 +3295,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -185,7 +185,7 @@ build_info:
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3279,7 +3279,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -267,7 +267,7 @@ build_info:
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3374,7 +3374,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- 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: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,7 +3229,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/concatRuns",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -168,7 +168,7 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3239,7 +3239,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- 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: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3465,7 +3465,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- 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: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/nextflow/utils/listInputDir"
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3317,7 +3317,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -214,7 +214,7 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3319,7 +3319,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -212,7 +212,7 @@ build_info:
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
  viash_version: "0.9.2"
-  git_commit: "3516346356891d56d98673343f9e61ab0919199e"
+  git_commit: "916971370f30aeb2e30ccaa9291d37958a2b01d0"
  git_remote: "https://github.com/viash-hub/htrnaseq"
 package_config:
  name: "htrnaseq"
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3299,7 +3299,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
    "viash_version" : "0.9.2",
-    "git_commit" : "3516346356891d56d98673343f9e61ab0919199e",
+    "git_commit" : "916971370f30aeb2e30ccaa9291d37958a2b01d0",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {