Build branch main with version main (ebb533e)

Build pipeline: viash-hub.htrnaseq.main-kchgg Source commit: ebb533e982 Source message: Add 'data_processed' subdir to output structure (#45)
2025-03-20 09:12:44 +00:00
parent df41c7466c
commit ee093a387e
60 changed files with 81 additions and 74 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,10 @@
+# htrnaseq v0.6.0
+
+## Breaking changes
+
+* `runner`: a subdirectory `data_processed` is now added to the output structure, in between
+  the experiment ID and the directory with the workflow date and version (PR #45).
+
 # htrnaseq v0.5.5

 ## New functionality
--- a/src/workflows/runner/main.nf
+++ b/src/workflows/runner/main.nf
@@ -85,7 +85,7 @@ workflow run_wf {
      //
      // So, we should combine everything together
      //
-      // project_id / experiment_id / date_workflow
+      // project_id / experiment_id / "data_processed" / date_workflow

      | toSortedList

@@ -115,7 +115,7 @@ workflow run_wf {
          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 : "${id0}/${date}"
+          def id1 = (state.plain_output) ? id : "${id0}/data_processed/${date}"
          def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}"

          if (id == id2) {
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/executable/eset/create_eset"
  executable: "target/executable/eset/create_eset/create_eset"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -477,9 +477,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 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="2025-02-28T13:27:08Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:13Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -177,7 +177,7 @@ build_info:
  output: "target/executable/eset/create_fdata"
  executable: "target/executable/eset/create_fdata/create_fdata"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -478,9 +478,9 @@ 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="2025-02-28T13:27:07Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:13Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -191,7 +191,7 @@ build_info:
  output: "target/executable/eset/create_pdata"
  executable: "target/executable/eset/create_pdata/create_pdata"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -488,9 +488,9 @@ 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="2025-02-28T13:27:09Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:13Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -148,7 +148,7 @@ build_info:
  output: "target/executable/integration_test_components/htrnaseq/check_eset"
  executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -470,9 +470,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 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="2025-02-28T13:27:09Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -158,7 +158,7 @@ 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: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -476,9 +476,9 @@ 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="2025-02-28T13:27:08Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -143,7 +143,7 @@ build_info:
  output: "target/executable/io/publish_fastqs"
  executable: "target/executable/io/publish_fastqs/publish_fastqs"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -470,9 +470,9 @@ 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="2025-02-28T13:27:08Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -187,7 +187,7 @@ build_info:
  output: "target/executable/io/publish_results"
  executable: "target/executable/io/publish_results/publish_results"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -484,9 +484,9 @@ 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="2025-02-28T13:27:07Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:13Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -279,7 +279,7 @@ build_info:
  output: "target/executable/parallel_map"
  executable: "target/executable/parallel_map/parallel_map"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -540,9 +540,9 @@ 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="2025-02-28T13:27:09Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:14Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -201,7 +201,7 @@ build_info:
  output: "target/executable/report/create_report"
  executable: "target/executable/report/create_report/create_report"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -476,9 +476,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag

 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="2025-02-28T13:27:08Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:14Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -198,7 +198,7 @@ build_info:
  output: "target/executable/stats/combine_star_logs"
  executable: "target/executable/stats/combine_star_logs/combine_star_logs"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -490,9 +490,9 @@ 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="2025-02-28T13:27:09Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -182,7 +182,7 @@ build_info:
  output: "target/executable/stats/generate_pool_statistics"
  executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -483,9 +483,9 @@ 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="2025-02-28T13:27:08Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -264,7 +264,7 @@ build_info:
  output: "target/executable/stats/generate_well_statistics"
  executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -520,9 +520,9 @@ 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="2025-02-28T13:27:08Z"
+LABEL org.opencontainers.image.created="2025-03-20T08:25:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
+LABEL org.opencontainers.image.revision="ebb533e98281cfd73643b91029d1759f26d69f55"
 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
@@ -198,7 +198,7 @@ build_info:
  output: "target/nextflow/eset/create_eset"
  executable: "target/nextflow/eset/create_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3072,7 +3072,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -177,7 +177,7 @@ build_info:
  output: "target/nextflow/eset/create_fdata"
  executable: "target/nextflow/eset/create_fdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3044,7 +3044,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_fdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -191,7 +191,7 @@ build_info:
  output: "target/nextflow/eset/create_pdata"
  executable: "target/nextflow/eset/create_pdata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3058,7 +3058,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/eset/create_pdata",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -148,7 +148,7 @@ build_info:
  output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
  executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -2997,7 +2997,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -158,7 +158,7 @@ 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: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3009,7 +3009,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -143,7 +143,7 @@ build_info:
  output: "target/nextflow/io/publish_fastqs"
  executable: "target/nextflow/io/publish_fastqs/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -2983,7 +2983,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_fastqs",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -187,7 +187,7 @@ build_info:
  output: "target/nextflow/io/publish_results"
  executable: "target/nextflow/io/publish_results/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3032,7 +3032,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/io/publish_results",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -279,7 +279,7 @@ build_info:
  output: "target/nextflow/parallel_map"
  executable: "target/nextflow/parallel_map/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3144,7 +3144,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/parallel_map",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -201,7 +201,7 @@ build_info:
  output: "target/nextflow/report/create_report"
  executable: "target/nextflow/report/create_report/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3077,7 +3077,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/report/create_report",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -198,7 +198,7 @@ build_info:
  output: "target/nextflow/stats/combine_star_logs"
  executable: "target/nextflow/stats/combine_star_logs/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3060,7 +3060,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/combine_star_logs",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -182,7 +182,7 @@ build_info:
  output: "target/nextflow/stats/generate_pool_statistics"
  executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3044,7 +3044,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_pool_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -264,7 +264,7 @@ build_info:
  output: "target/nextflow/stats/generate_well_statistics"
  executable: "target/nextflow/stats/generate_well_statistics/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3139,7 +3139,7 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/stats/generate_well_statistics",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -165,7 +165,7 @@ build_info:
  output: "target/nextflow/utils/listInputDir"
  executable: "target/nextflow/utils/listInputDir/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3004,7 +3004,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/utils/listInputDir",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -323,7 +323,7 @@ build_info:
  output: "target/nextflow/workflows/htrnaseq"
  executable: "target/nextflow/workflows/htrnaseq/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3229,7 +3229,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/htrnaseq",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -218,7 +218,7 @@ build_info:
  output: "target/nextflow/workflows/runner"
  executable: "target/nextflow/workflows/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3082,7 +3082,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3220,7 +3220,7 @@ workflow run_wf {
      //
      // So, we should combine everything together
      //
-      // project_id / experiment_id / date_workflow
+      // project_id / experiment_id / "data_processed" / date_workflow

      | toSortedList

@@ -3250,7 +3250,7 @@ workflow run_wf {
          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 : "${id0}/${date}"
+          def id1 = (state.plain_output) ? id : "${id0}/data_processed/${date}"
          def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}"

          if (id == id2) {
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -211,7 +211,7 @@ build_info:
  output: "target/nextflow/workflows/well_demultiplex"
  executable: "target/nextflow/workflows/well_demultiplex/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3084,7 +3084,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_demultiplex",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "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
@@ -209,7 +209,7 @@ build_info:
  output: "target/nextflow/workflows/well_metadata"
  executable: "target/nextflow/workflows/well_metadata/main.nf"
  viash_version: "0.9.0"
-  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
+  git_commit: "ebb533e98281cfd73643b91029d1759f26d69f55"
  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
@@ -3064,7 +3064,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/well_metadata",
    "viash_version" : "0.9.0",
-    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
+    "git_commit" : "ebb533e98281cfd73643b91029d1759f26d69f55",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {