Build branch main with version main (10d3b38)

Build pipeline: viash-hub.htrnaseq.main-77sg6 Source commit: 10d3b382d6 Source message: Add runner integration tests, revert ec0dd8b (#64)
2025-08-01 10:14:18 +00:00
parent 060c9c49a8
commit 6f76b49468
71 changed files with 373 additions and 217 deletions
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -206,9 +206,9 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:43Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:43Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -197,9 +197,9 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:43Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -155,9 +155,9 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:44Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
+++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml
@@ -164,9 +164,9 @@ 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: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:44Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish_fastqs/.config.vsh.yaml
+++ b/target/executable/io/publish_fastqs/.config.vsh.yaml
@@ -139,9 +139,9 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:43Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/io/publish_results/.config.vsh.yaml
+++ b/target/executable/io/publish_results/.config.vsh.yaml
@@ -202,9 +202,9 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:43Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -285,9 +285,9 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:44Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/executable/report/create_report/create_report
+++ b/target/executable/report/create_report/create_report
@@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR

 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -204,9 +204,9 @@ build_info:
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:42Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -188,9 +188,9 @@ build_info:
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:42Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -270,9 +270,9 @@ build_info:
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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="2025-07-29T10:37:42Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/utils/save_params/.config.vsh.yaml
+++ b/target/executable/utils/save_params/.config.vsh.yaml
@@ -151,9 +151,9 @@ build_info:
  output: "target/executable/utils/save_params"
  executable: "target/executable/utils/save_params/save_params"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/executable/utils/save_params/save_params
+++ b/target/executable/utils/save_params/save_params
@@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "pyyaml"

 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z"
+LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160"
+LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -206,9 +206,9 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3309,9 +3309,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3279,9 +3279,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -197,9 +197,9 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3293,9 +3293,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -155,9 +155,9 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -3233,9 +3233,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- 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
@@ -164,9 +164,9 @@ 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: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- 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
@@ -3244,9 +3244,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml
+++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml
@@ -139,9 +139,9 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/io/publish_fastqs/main.nf
+++ b/target/nextflow/io/publish_fastqs/main.nf
@@ -3207,9 +3207,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/io/publish_results/.config.vsh.yaml
+++ b/target/nextflow/io/publish_results/.config.vsh.yaml
@@ -202,9 +202,9 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/io/publish_results/main.nf
+++ b/target/nextflow/io/publish_results/main.nf
@@ -3277,9 +3277,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -285,9 +285,9 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -3379,9 +3379,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3323,9 +3323,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -204,9 +204,9 @@ build_info:
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3295,9 +3295,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -188,9 +188,9 @@ build_info:
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3279,9 +3279,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -270,9 +270,9 @@ build_info:
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3374,9 +3374,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/utils/concatRuns/.config.vsh.yaml
+++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml
@@ -160,9 +160,9 @@ build_info:
  output: "target/nextflow/utils/concatRuns"
  executable: "target/nextflow/utils/concatRuns/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
  dependencies:
  - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
 package_config:
--- a/target/nextflow/utils/concatRuns/main.nf
+++ b/target/nextflow/utils/concatRuns/main.nf
@@ -3229,9 +3229,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/concatRuns",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/utils/listInputDir/.config.vsh.yaml
+++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml
@@ -171,9 +171,9 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/utils/listInputDir/main.nf
+++ b/target/nextflow/utils/listInputDir/main.nf
@@ -3239,9 +3239,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/utils/save_params/.config.vsh.yaml
+++ b/target/nextflow/utils/save_params/.config.vsh.yaml
@@ -151,9 +151,9 @@ build_info:
  output: "target/nextflow/utils/save_params"
  executable: "target/nextflow/utils/save_params/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/utils/save_params/main.nf
+++ b/target/nextflow/utils/save_params/main.nf
@@ -3223,9 +3223,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/utils/save_params",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -345,9 +345,9 @@ build_info:
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
  dependencies:
  - "target/nextflow/stats/combine_star_logs"
  - "target/nextflow/stats/generate_pool_statistics"
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -3484,9 +3484,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/workflows/runner/.config.vsh.yaml
+++ b/target/nextflow/workflows/runner/.config.vsh.yaml
@@ -99,14 +99,6 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
- name: "Annotation flags"
-  arguments:
-  - type: "boolean_true"
-    name: "--plain_output"
-    description: "Flag to indicate that the output should be stored directly under\
-      \ $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n"
-    info: null
-    direction: "input"
 - name: "Publish arguments"
  arguments:
  - type: "string"
@@ -135,6 +127,11 @@ resources:
  path: "_viash.yaml"
  dest: "_viash.yaml"
 description: "Runner for HT RNA-seq pipeline"
+test_resources:
+- type: "nextflow_script"
+  path: "test.nf"
+  is_executable: true
+  entrypoint: "test_wf"
 info: null
 status: "enabled"
 scope:
@@ -238,9 +235,9 @@ build_info:
  output: "target/nextflow/workflows/runner"
  executable: "target/nextflow/workflows/runner/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
  dependencies:
  - "target/nextflow/utils/listInputDir"
  - "target/nextflow/workflows/htrnaseq"
--- a/target/nextflow/workflows/runner/main.nf
+++ b/target/nextflow/workflows/runner/main.nf
@@ -3150,17 +3150,6 @@ meta = [
        }
      ]
    },
-    {
-      "name" : "Annotation flags",
-      "arguments" : [
-        {
-          "type" : "boolean_true",
-          "name" : "--plain_output",
-          "description" : "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
-          "direction" : "input"
-        }
-      ]
-    },
    {
      "name" : "Publish arguments",
      "arguments" : [
@@ -3202,6 +3191,14 @@ meta = [
    }
  ],
  "description" : "Runner for HT RNA-seq pipeline",
+  "test_resources" : [
+    {
+      "type" : "nextflow_script",
+      "path" : "test.nf",
+      "is_executable" : true,
+      "entrypoint" : "test_wf"
+    }
+  ],
  "status" : "enabled",
  "scope" : {
    "image" : "public",
@@ -3336,9 +3333,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
@@ -3551,20 +3548,10 @@ workflow run_wf {
    results_publish_ch = grouped_with_params_list_ch
      | publish_results.run(
        fromState: { id, state ->
-          def project = (state.plain_output) ? id : "${state.project_id}"
-          def experiment = (state.plain_output) ? id : "${state.experiment_id}"
-          def id0 = "${project}/${experiment}"
-          def id1 = (state.plain_output) ? id : "${id0}/data_processed/${date}"
-          def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}"
-
-          if (id == id2) {
-            println("Publising results to ${params.results_publish_dir}")
-          } else {
-            println("Publising results to ${params.results_publish_dir}/${id2}")
-          }
+          def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
+          println("Publising results to ${params.results_publish_dir}/${output_dir}")

          [
-            star_output: state.star_output,
            star_output: state.star_output,
            nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom,
            star_qc_metrics: state.star_qc_metrics,
@@ -3573,7 +3560,7 @@ workflow run_wf {
            p_data: state.p_data,
            html_report: state.html_report,
            run_params: state.run_params,
-            output: "${id2}"
+            output: output_dir.toString()
          ]
        },
        toState: { id, result, state -> state },
@@ -3604,19 +3591,12 @@ workflow run_wf {
      }
      | publish_fastqs.run(
        fromState: { id, state ->
-          def id0 = state.run_id
-          def id1 = (state.plain_output) ? id : "${id0}/${date}"
-          def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}/${state.sample_id}"
-
-          if (id == id2) {
-            println("Publising fastqs to ${params.fastq_publish_dir}")
-          } else {
-            println("Publising fastqs to ${params.fastq_publish_dir}/${id2}")
-          }
+          def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"
+          println("Publising fastqs to ${params.fastq_publish_dir}/${output_dir}")

          [
            input: state.fastq_output,
-            output: "${id2}",
+            output: output_dir.toString(),
          ]
        },
        toState: { id, result, state -> state },
--- a/target/nextflow/workflows/runner/nextflow_schema.json
+++ b/target/nextflow/workflows/runner/nextflow_schema.json
@@ -85,19 +85,6 @@
        }
      }
    },
-    "annotation flags": {
-      "title": "Annotation flags",
-      "type": "object",
-      "description": "No description",
-      "properties": {
-        "plain_output": {
-          "type": "boolean",
-          "description": "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/<date_time>_demultiplex_<version>/.\n",
-          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
-          "default": false
-        }
-      }
-    },
    "publish arguments": {
      "title": "Publish arguments",
      "type": "object",
@@ -135,9 +122,6 @@
    {
      "$ref": "#/$defs/metadata arguments"
    },
-    {
-      "$ref": "#/$defs/annotation flags"
-    },
    {
      "$ref": "#/$defs/publish arguments"
    },
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -217,9 +217,9 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt"
  - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3319,9 +3319,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",
--- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml
@@ -215,9 +215,9 @@ build_info:
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
  viash_version: "0.9.4"
-  git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160"
+  git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2"
  git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-9-g0e87de8"
+  git_tag: "v0.7.2-11-g10d3b38"
 package_config:
  name: "htrnaseq"
  version: "main"
--- a/target/nextflow/workflows/well_metadata/main.nf
+++ b/target/nextflow/workflows/well_metadata/main.nf
@@ -3299,9 +3299,9 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
    "viash_version" : "0.9.4",
-    "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160",
+    "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2",
    "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-9-g0e87de8"
+    "git_tag" : "v0.7.2-11-g10d3b38"
  },
  "package_config" : {
    "name" : "htrnaseq",