Build branch main with version main (8dff52a)

Build pipeline: viash-hub.htrnaseq.main-j2rpn Source commit: 8dff52a885 Source message: Add `umi_length` parameter to runner. (#46)
2025-02-28 14:10:10 +00:00
parent e5a3fd36ee
commit df41c7466c
62 changed files with 119 additions and 70 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,9 @@
+# htrnaseq v0.5.5
+
+## New functionality
+
+* Add `umi_length` parameter to the `runner` workflow (PR #46)
+
 # htrnaseq v0.5.4

 * Fix missing barcodes in the output from `generate_pool_statistics`, which caused an assertion error in `create_pdata`.
--- a/src/workflows/runner/config.vsh.yaml
+++ b/src/workflows/runner/config.vsh.yaml
@@ -23,6 +23,12 @@ argument_groups:
        type: string
        multiple: true
        default: ["Undetermined"]
+      - name: "--umi_length"
+        description: |
+          Length of the UMI sequences
+        type: integer
+        min: 1
+        default: 10
  - name: Metadata arguments
    arguments:
      - name: --id
--- a/src/workflows/runner/main.nf
+++ b/src/workflows/runner/main.nf
@@ -75,6 +75,7 @@ workflow run_wf {
          barcodesFasta: "barcodesFasta",
          genomeDir: "genomeDir",
          annotation: "annotation",
+          umi_length: "umi_length",
        ],
        toState: { id, result, state -> state + result }
      )
--- 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:30Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:30Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:07Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:30Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:30Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:30Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:28Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:29Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:07Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:31Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:31Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:28Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:09Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:29Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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="2025-02-21T11:03:29Z"
+LABEL org.opencontainers.image.created="2025-02-28T13:27:08Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="bd5b2d41718677ee367d3829447241df9733c8d3"
+LABEL org.opencontainers.image.revision="8dff52a8854120e919b3701b9501b3acbf01c65b"
 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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
@@ -51,6 +51,17 @@ argument_groups:
    direction: "input"
    multiple: true
    multiple_sep: ";"
+  - type: "integer"
+    name: "--umi_length"
+    description: "Length of the UMI sequences\n"
+    info: null
+    default:
+    - 10
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
 - name: "Metadata arguments"
  arguments:
  - type: "string"
@@ -207,7 +218,7 @@ build_info:
  output: "target/nextflow/workflows/runner"
  executable: "target/nextflow/workflows/runner/main.nf"
  viash_version: "0.9.0"
-  git_commit: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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
@@ -2863,6 +2863,19 @@ meta = [
          "direction" : "input",
          "multiple" : true,
          "multiple_sep" : ";"
+        },
+        {
+          "type" : "integer",
+          "name" : "--umi_length",
+          "description" : "Length of the UMI sequences\n",
+          "default" : [
+            10
+          ],
+          "required" : false,
+          "min" : 1,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
        }
      ]
    },
@@ -3069,7 +3082,7 @@ meta = [
    "engine" : "native|native",
    "output" : "target/nextflow/workflows/runner",
    "viash_version" : "0.9.0",
-    "git_commit" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {
@@ -3197,6 +3210,7 @@ workflow run_wf {
          barcodesFasta: "barcodesFasta",
          genomeDir: "genomeDir",
          annotation: "annotation",
+          umi_length: "umi_length",
        ],
        toState: { id, result, state -> state + result }
      )
--- a/target/nextflow/workflows/runner/nextflow_schema.json
+++ b/target/nextflow/workflows/runner/nextflow_schema.json
@@ -64,6 +64,17 @@
            }
    

+        ,
+                "umi_length": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, default: `10`. Length of the UMI sequences\n",
+                "help_text": "Type: `integer`, default: `10`. Length of the UMI sequences\n"
+            ,
+                "default":10
+            }
+    
+
 }
 },
    
--- 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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "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: "bd5b2d41718677ee367d3829447241df9733c8d3"
+  git_commit: "8dff52a8854120e919b3701b9501b3acbf01c65b"
  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" : "bd5b2d41718677ee367d3829447241df9733c8d3",
+    "git_commit" : "8dff52a8854120e919b3701b9501b3acbf01c65b",
    "git_remote" : "https://github.com/viash-hub/htrnaseq"
  },
  "package_config" : {