diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0144070e..85b3df47 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,9 +1,20 @@
 # demultiplex v0.x.x
 
+# New functionality
+
+* Added `umi_length` argument (PR #27).
+
+# Breaking changes
+
+* Removed `wellBarcodesLength` from `parallel_map` workflow (PR #27).
+
 # Minor changes
 
 * Use `v0.3.0` version of cutadapt instead of `main` (PR #23 and PR #24).
 
+* `create_eset`: Update base container image, `R` version and all dependencies
+  to newer versions (PR #28).
+
 # demultiplex v0.2.0
 
 # New functionality
diff --git a/src/eset/create_eset/config.vsh.yaml b/src/eset/create_eset/config.vsh.yaml
index 194c2bce..f7837482 100644
--- a/src/eset/create_eset/config.vsh.yaml
+++ b/src/eset/create_eset/config.vsh.yaml
@@ -37,41 +37,18 @@ test_resources:
   - path: test_data/mapping_dir
 engines:
   - type: docker
-    image: r-base:4.3.0
+    image: rocker/r2u:24.04
     setup:
-      - type: apt
-        packages: # most of these are required for devtools
-          - libcurl4-openssl-dev
-          - libssl-dev
-          - libxml2-dev
-          - libfftw3-dev # Seurat
-          - libfontconfig1-dev # Seurat
-          - libfreetype-dev # Seurat
-          - libhdf5-dev # Seurat
-          - bzip2 # Seurat
-          - libharfbuzz-dev # Seurat
-          - libfribidi-dev # Seurat
-          - libtiff-dev # Seurat
-          - libgsl-dev # Seurat
-          - libcairo-dev # Seurat
-          - libudunits2-dev # SeuratObject
-          - procps
       - type: r
         cran:
           - data.table
-          - BiocManager
-          - remotes
-        bioc:
-          - Biobase
-          - limma  # dependency for nlcv 
-          - a4Core # dependency for nlcv 
-          - MLInterfaces # dependency for nlcv 
-          - multtest # dependency for nlcv
-        cran:
           - nlcv
-        script: |
-            remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz", dependencies=TRUE, upgrade_dependencies=FALSE);\
-            remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz", repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\
+        bioc:
+          - Seurat
+    test_setup:
+      - type: r
+        cran:
+          - testthat
 runners:
   - type: executable
   - type: nextflow
diff --git a/src/eset/create_eset/script.R b/src/eset/create_eset/script.R
index 22765082..9e55d22c 100644
--- a/src/eset/create_eset/script.R
+++ b/src/eset/create_eset/script.R
@@ -217,7 +217,7 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
   requireNamespace("Seurat")
   seurat_object <- Seurat::CreateSeuratObject(counts = read_matrix)
 
-  exprs_matrix <- as.matrix(seurat_object[['RNA']]@counts)
+  exprs_matrix <- as.matrix(seurat_object[['RNA']]$counts)
   # replace "-" with "_" for features with "_" 
   # before converting to Seurat object
   rownames(exprs_matrix)[idx] <- gsub("-", "_", rownames(exprs_matrix)[idx])
diff --git a/src/parallel_map/config.vsh.yaml b/src/parallel_map/config.vsh.yaml
index aee6457f..867bef71 100644
--- a/src/parallel_map/config.vsh.yaml
+++ b/src/parallel_map/config.vsh.yaml
@@ -35,10 +35,6 @@ argument_groups:
       description: The barcodes/wells to process
   - name: Barcode arguments
     arguments:
-    - name: "--wellBarcodesLength"
-      type: integer
-      required: true
-      description: The length of the well barcodes
     - name: "--umiLength"
       type: integer
       required: true
diff --git a/src/parallel_map/script.sh b/src/parallel_map/script.sh
index 72ef79ac..ce7468b7 100755
--- a/src/parallel_map/script.sh
+++ b/src/parallel_map/script.sh
@@ -6,7 +6,6 @@ par_input_r2="work/2c/5b8b3a2dd4a988b8838e3f72d38a37/_viash_par/input_r2_1/two__
 par_barcodes="ACACCGAATT;GGCTATTGAT"
 par_output="./*"
 par_genomeDir="star"
-par_wellBarcodesLength=10
 par_umiLength=10
 par_limitBAMsortRAM="10000000000"
 meta_cpus=2
@@ -73,16 +72,17 @@ fi
 
 # Define the function that will be used to run a single job
 function _run() {
-  local par_wellBarcodeLength="$1"
-  local par_UMIlength="$2"
-  local par_output="$3"
-  local par_genomeDir="$4"
-  local par_limitBAMsortRAM="$5"
-  local par_runThreadN="$6"
-  local barcode="$7"
-  local input_R1="$8"
-  local input_R2="$9"
-  local par_UMIstart=$(($par_wellBarcodeLength + 1))
+  local par_UMIlength="$1"
+  local par_output="$2"
+  local par_genomeDir="$3"
+  local par_limitBAMsortRAM="$4"
+  local par_runThreadN="$5"
+  local barcode="$6"
+  local input_R1="$7"
+  local input_R2="$8"
+
+  local barcode_length="${#barcode}"
+  local umi_start="$(($barcode_length + 1))"
 
   set -eo pipefail
 
@@ -178,8 +178,8 @@ function _run() {
     --outSAMtype BAM SortedByCoordinate \
     --soloCBstart 1 \
     --readFilesType "Fastx" \
-    --soloCBlen "$par_wellBarcodeLength" \
-    --soloUMIstart "$par_UMIstart" \
+    --soloCBlen "$barcode_length" \
+    --soloUMIstart "$umi_start" \
     --soloUMIlen "$par_UMIlength" \
     --soloBarcodeReadLength 0 \
     --soloStrand Unstranded \
@@ -235,7 +235,7 @@ parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
               "--joblog" "$par_joblog" "_run" "{}")
 
 # Arguments for which there is one value, so these will not create extra jobs
-parallel_cmd+=(":::" "$par_wellBarcodesLength" ":::" "$par_umiLength" ":::" "$par_output" ":::" "$par_genomeDir" ":::" "$par_limitBAMsortRAM" ":::" "$par_runThreadN")
+parallel_cmd+=(":::" "$par_umiLength" ":::" "$par_output" ":::" "$par_genomeDir" ":::" "$par_limitBAMsortRAM" ":::" "$par_runThreadN")
 
 # Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
 # Thus, these argument lists should have the same length.
diff --git a/src/parallel_map/test.sh b/src/parallel_map/test.sh
index 1c8cc37e..da49a295 100755
--- a/src/parallel_map/test.sh
+++ b/src/parallel_map/test.sh
@@ -110,7 +110,6 @@ pushd "$run_1_dir" > /dev/null
     --input_r2 "$TMPDIR/sample1_R2.fastq;$TMPDIR/sample2_R2.fastq" \
     --genomeDir "$TMPDIR/index/" \
     --barcodes "ACAGTCACAG;CGGGTTTACC" \
-    --wellBarcodesLength 10 \
     --umiLength 10 \
     --runThreadN 2 \
     --output "$TMPDIR/output_*" > /dev/null 2>&1 
@@ -203,7 +202,6 @@ pushd "$run_2_dir" > /dev/null
     --input_r2 "$TMPDIR/sample1_R2.fastq.gz;$TMPDIR/sample2_R2.fastq.gz" \
     --genomeDir "$TMPDIR/index/" \
     --barcodes "ACAGTCACAG;CGGGTTTACC" \
-    --wellBarcodesLength 10 \
     --umiLength 10 \
     --runThreadN 2 \
     --output "$TMPDIR/output_gz_*" > /dev/null 2>&1
@@ -293,7 +291,6 @@ set +eo pipefail
     --input_r2 "$TMPDIR/sample1_R2.fastq.gz;$TMPDIR/sample2_R2.fastq.gz" \
     --genomeDir "$TMPDIR/index/" \
     --barcodes "ACAGTCACAG" \
-    --wellBarcodesLength 10 \
     --umiLength 10 \
     --runThreadN 2 \
     --output "$TMPDIR/output_gz_*" > /dev/null 2>&1 && echo "Expected non-zero exit code " && exit 1
@@ -310,7 +307,6 @@ set +eo pipefail
     --input_r2 "$TMPDIR/sample1_R2.fastq.gz;$TMPDIR/sample2_R2.fastq.gz" \
     --genomeDir "$TMPDIR/index/" \
     --barcodes "ACAGTCACAG;CGGGTTTACC" \
-    --wellBarcodesLength 10 \
     --umiLength 10 \
     --runThreadN 2 \
     --output "$TMPDIR/output_run4" > /dev/null 2>&1 && echo "Expected non-zero exit code." && exit 1 
@@ -329,7 +325,6 @@ set +eo pipefail
     --input_r2 "$TMPDIR/sample1_R2.fastq;$TMPDIR/sample2_R2.fastq" \
     --genomeDir "$TMPDIR/index/" \
     --barcodes "ACAGTCACAG;CGGGTTTACC" \
-    --wellBarcodesLength 10 \
     --umiLength 10 \
     --runThreadN 2 \
     --output "$TMPDIR/output_run5_*" > /dev/null 2>&1 && echo "Expected non-zero exit code " && exit 1
@@ -346,7 +341,6 @@ set +eo pipefail
     --input_r2 "$TMPDIR/sample1_R2.fastq;$TMPDIR/sample2_R2.fastq" \
     --genomeDir "$TMPDIR/index/" \
     --barcodes "ACAGTCACAG;CGGGTTTACC" \
-    --wellBarcodesLength 10 \
     --umiLength 10 \
     --runThreadN 2 \
     --output "$TMPDIR/output_run_6_*" > /dev/null 2>&1 && echo "Expected non-zero exit code " && exit 1
diff --git a/src/workflows/htrnaseq/config.vsh.yaml b/src/workflows/htrnaseq/config.vsh.yaml
index e92f13ba..3ef6aec0 100644
--- a/src/workflows/htrnaseq/config.vsh.yaml
+++ b/src/workflows/htrnaseq/config.vsh.yaml
@@ -23,6 +23,12 @@ argument_groups:
       - name: --barcodesFasta
         type: file
         required: true
+      - name: "--umi_length"
+        description: |
+          Length of the UMI sequences
+        type: integer
+        min: 1
+        default: 10
       - name: --genomeDir
         type: file
         required: true
diff --git a/src/workflows/htrnaseq/main.nf b/src/workflows/htrnaseq/main.nf
index d6c1d64c..4e7b4dac 100644
--- a/src/workflows/htrnaseq/main.nf
+++ b/src/workflows/htrnaseq/main.nf
@@ -37,6 +37,7 @@ workflow run_wf {
             "input_r1": state.fastq_output_r1[0],
             "input_r2": state.fastq_output_r2[0],
             "barcode": state.barcode,
+            "umi_length": state.umi_length,
             "pool": state.pool,
             "output": state.star_output[0],
             "genomeDir": state.genomeDir,
diff --git a/src/workflows/parallel_map_wf/config.vsh.yaml b/src/workflows/parallel_map_wf/config.vsh.yaml
index 563ae1ce..87a49e7f 100644
--- a/src/workflows/parallel_map_wf/config.vsh.yaml
+++ b/src/workflows/parallel_map_wf/config.vsh.yaml
@@ -22,6 +22,9 @@ argument_groups:
       - name: "--barcode"
         type: string
         required: true
+      - name: "--umi_length"
+        type: integer
+        min: 1
       - name: "--pool"
         type: string
         required: true
diff --git a/src/workflows/parallel_map_wf/main.nf b/src/workflows/parallel_map_wf/main.nf
index c1c03f11..0c9e9aec 100644
--- a/src/workflows/parallel_map_wf/main.nf
+++ b/src/workflows/parallel_map_wf/main.nf
@@ -25,8 +25,7 @@ workflow run_wf {
            "genomeDir": state.genomeDir,
            "barcodes": state.wells,
            "pool": state.pool,
-           "wellBarcodesLength": 10,
-           "umiLength": 10,
+           "umiLength": state.umi_length,
            "output": state.output,
          ]
         },
diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml
index 01525f98..8ed1358b 100644
--- a/target/executable/eset/create_eset/.config.vsh.yaml
+++ b/target/executable/eset/create_eset/.config.vsh.yaml
@@ -170,44 +170,22 @@ runners:
 engines:
 - type: "docker"
   id: "docker"
-  image: "r-base:4.3.0"
+  image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
   target_tag: "main"
   namespace_separator: "/"
   setup:
-  - type: "apt"
-    packages:
-    - "libcurl4-openssl-dev"
-    - "libssl-dev"
-    - "libxml2-dev"
-    - "libfftw3-dev"
-    - "libfontconfig1-dev"
-    - "libfreetype-dev"
-    - "libhdf5-dev"
-    - "bzip2"
-    - "libharfbuzz-dev"
-    - "libfribidi-dev"
-    - "libtiff-dev"
-    - "libgsl-dev"
-    - "libcairo-dev"
-    - "libudunits2-dev"
-    - "procps"
-    interactive: false
   - type: "r"
     cran:
+    - "data.table"
     - "nlcv"
     bioc:
-    - "Biobase"
-    - "limma"
-    - "a4Core"
-    - "MLInterfaces"
-    - "multtest"
-    script:
-    - "remotes::install_url(\"https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz\"\
-      , dependencies=TRUE, upgrade_dependencies=FALSE);\\\nremotes::install_url(\"\
-      https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz\"\
-      , repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\\\
-      \n"
+    - "Seurat"
+    bioc_force_install: false
+  test_setup:
+  - type: "r"
+    cran:
+    - "testthat"
     bioc_force_install: false
   entrypoint: []
   cmd: null
@@ -220,8 +198,8 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset
index 3bd4536d..5f33985f 100755
--- a/target/executable/eset/create_eset/create_eset
+++ b/target/executable/eset/create_eset/create_eset
@@ -468,29 +468,18 @@ function ViashDockerfile {
 
   if [[ "$engine_id" == "docker" ]]; then
     cat << 'VIASHDOCKER'
-FROM r-base:4.3.0
+FROM rocker/r2u:24.04
 ENTRYPOINT []
-RUN apt-get update && \
-  DEBIAN_FRONTEND=noninteractive apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libfftw3-dev libfontconfig1-dev libfreetype-dev libhdf5-dev bzip2 libharfbuzz-dev libfribidi-dev libtiff-dev libgsl-dev libcairo-dev libudunits2-dev procps && \
-  rm -rf /var/lib/apt/lists/*
-
 RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
   Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
-  Rscript -e 'if (!requireNamespace("Biobase", quietly = TRUE)) BiocManager::install("Biobase")' && \
-  Rscript -e 'if (!requireNamespace("limma", quietly = TRUE)) BiocManager::install("limma")' && \
-  Rscript -e 'if (!requireNamespace("a4Core", quietly = TRUE)) BiocManager::install("a4Core")' && \
-  Rscript -e 'if (!requireNamespace("MLInterfaces", quietly = TRUE)) BiocManager::install("MLInterfaces")' && \
-  Rscript -e 'if (!requireNamespace("multtest", quietly = TRUE)) BiocManager::install("multtest")' && \
-  Rscript -e 'remotes::install_cran(c("nlcv"), repos = "https://cran.rstudio.com")' && \
-  Rscript -e 'remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz", dependencies=TRUE, upgrade_dependencies=FALSE);\
-remotes::install_url("https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz", repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\
-'
+  Rscript -e 'if (!requireNamespace("Seurat", quietly = TRUE)) BiocManager::install("Seurat")' && \
+  Rscript -e 'remotes::install_cran(c("data.table", "nlcv"), repos = "https://cran.rstudio.com")'
 
 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="2025-01-10T15:09:09Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -1362,7 +1351,7 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
   requireNamespace("Seurat")
   seurat_object <- Seurat::CreateSeuratObject(counts = read_matrix)
 
-  exprs_matrix <- as.matrix(seurat_object[['RNA']]@counts)
+  exprs_matrix <- as.matrix(seurat_object[['RNA']]\$counts)
   # replace "-" with "_" for features with "_" 
   # before converting to Seurat object
   rownames(exprs_matrix)[idx] <- gsub("-", "_", rownames(exprs_matrix)[idx])
diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml
index c18fff35..454b1959 100644
--- a/target/executable/eset/create_fdata/.config.vsh.yaml
+++ b/target/executable/eset/create_fdata/.config.vsh.yaml
@@ -177,8 +177,8 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata
index 253211b1..eeeadef2 100755
--- 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="2025-01-10T15:09:10Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml
index ea1b96b3..b4bb8bff 100644
--- a/target/executable/eset/create_pdata/.config.vsh.yaml
+++ b/target/executable/eset/create_pdata/.config.vsh.yaml
@@ -191,8 +191,8 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata
index a9e51a55..7600d6b4 100755
--- 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="2025-01-10T15:09:08Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 4583da32..14ed20c5 100644
--- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -148,8 +148,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset
index 77d76bfc..9b922a36 100755
--- 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="2025-01-10T15:09:10Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git 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
index 935a59aa..b2d41793 100644
--- 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
@@ -158,8 +158,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git 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
index 08e4e03d..378fd110 100755
--- 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="2025-01-10T15:09:10Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml
index 2d76721d..0ba5185f 100644
--- a/target/executable/parallel_map/.config.vsh.yaml
+++ b/target/executable/parallel_map/.config.vsh.yaml
@@ -68,14 +68,6 @@ argument_groups:
     multiple_sep: ";"
 - name: "Barcode arguments"
   arguments:
-  - type: "integer"
-    name: "--wellBarcodesLength"
-    description: "The length of the well barcodes"
-    info: null
-    required: true
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
   - type: "integer"
     name: "--umiLength"
     description: "The length of the UMIs"
@@ -264,8 +256,8 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map
index a9d82ab6..24119547 100755
--- a/target/executable/parallel_map/parallel_map
+++ b/target/executable/parallel_map/parallel_map
@@ -197,10 +197,6 @@ function ViashHelp {
   echo "        The barcodes/wells to process"
   echo ""
   echo "Barcode arguments:"
-  echo "    --wellBarcodesLength"
-  echo "        type: integer, required parameter"
-  echo "        The length of the well barcodes"
-  echo ""
   echo "    --umiLength"
   echo "        type: integer, required parameter"
   echo "        The length of the UMIs"
@@ -517,9 +513,9 @@ 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="2025-01-10T15:09:09Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
@@ -721,17 +717,6 @@ while [[ $# -gt 0 ]]; do
             fi
             shift 1
             ;;
-        --wellBarcodesLength)
-            [ -n "$VIASH_PAR_WELLBARCODESLENGTH" ] && ViashError Bad arguments for option \'--wellBarcodesLength\': \'$VIASH_PAR_WELLBARCODESLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_WELLBARCODESLENGTH="$2"
-            [ $# -lt 2 ] && ViashError Not enough arguments passed to --wellBarcodesLength. Use "--help" to get more information on the parameters. && exit 1
-            shift 2
-            ;;
-        --wellBarcodesLength=*)
-            [ -n "$VIASH_PAR_WELLBARCODESLENGTH" ] && ViashError Bad arguments for option \'--wellBarcodesLength=*\': \'$VIASH_PAR_WELLBARCODESLENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
-            VIASH_PAR_WELLBARCODESLENGTH=$(ViashRemoveFlags "$1")
-            shift 1
-            ;;
         --umiLength)
             [ -n "$VIASH_PAR_UMILENGTH" ] && ViashError Bad arguments for option \'--umiLength\': \'$VIASH_PAR_UMILENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
             VIASH_PAR_UMILENGTH="$2"
@@ -975,10 +960,6 @@ if [ -z ${VIASH_PAR_BARCODES+x} ]; then
   ViashError '--barcodes' is a required argument. Use "--help" to get more information on the parameters.
   exit 1
 fi
-if [ -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then
-  ViashError '--wellBarcodesLength' is a required argument. Use "--help" to get more information on the parameters.
-  exit 1
-fi
 if [ -z ${VIASH_PAR_UMILENGTH+x} ]; then
   ViashError '--umiLength' is a required argument. Use "--help" to get more information on the parameters.
   exit 1
@@ -1054,12 +1035,6 @@ if [ ! -z "$VIASH_PAR_GENOMEDIR" ] && [ ! -e "$VIASH_PAR_GENOMEDIR" ]; then
 fi
 
 # check whether parameters values are of the right type
-if [[ -n "$VIASH_PAR_WELLBARCODESLENGTH" ]]; then
-  if ! [[ "$VIASH_PAR_WELLBARCODESLENGTH" =~ ^[-+]?[0-9]+$ ]]; then
-    ViashError '--wellBarcodesLength' has to be an integer. Use "--help" to get more information on the parameters.
-    exit 1
-  fi
-fi
 if [[ -n "$VIASH_PAR_UMILENGTH" ]]; then
   if ! [[ "$VIASH_PAR_UMILENGTH" =~ ^[-+]?[0-9]+$ ]]; then
     ViashError '--umiLength' has to be an integer. Use "--help" to get more information on the parameters.
@@ -1289,7 +1264,6 @@ $( if [ ! -z ${VIASH_PAR_INPUT_R1+x} ]; then echo "${VIASH_PAR_INPUT_R1}" | sed
 $( if [ ! -z ${VIASH_PAR_INPUT_R2+x} ]; then echo "${VIASH_PAR_INPUT_R2}" | sed "s#'#'\"'\"'#g;s#.*#par_input_r2='&'#" ; else echo "# par_input_r2="; fi )
 $( if [ ! -z ${VIASH_PAR_GENOMEDIR+x} ]; then echo "${VIASH_PAR_GENOMEDIR}" | sed "s#'#'\"'\"'#g;s#.*#par_genomeDir='&'#" ; else echo "# par_genomeDir="; fi )
 $( if [ ! -z ${VIASH_PAR_BARCODES+x} ]; then echo "${VIASH_PAR_BARCODES}" | sed "s#'#'\"'\"'#g;s#.*#par_barcodes='&'#" ; else echo "# par_barcodes="; fi )
-$( if [ ! -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then echo "${VIASH_PAR_WELLBARCODESLENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_wellBarcodesLength='&'#" ; else echo "# par_wellBarcodesLength="; fi )
 $( if [ ! -z ${VIASH_PAR_UMILENGTH+x} ]; then echo "${VIASH_PAR_UMILENGTH}" | sed "s#'#'\"'\"'#g;s#.*#par_umiLength='&'#" ; else echo "# par_umiLength="; fi )
 $( if [ ! -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then echo "${VIASH_PAR_LIMITBAMSORTRAM}" | sed "s#'#'\"'\"'#g;s#.*#par_limitBAMsortRAM='&'#" ; else echo "# par_limitBAMsortRAM="; fi )
 $( if [ ! -z ${VIASH_PAR_RUNTHREADN+x} ]; then echo "${VIASH_PAR_RUNTHREADN}" | sed "s#'#'\"'\"'#g;s#.*#par_runThreadN='&'#" ; else echo "# par_runThreadN="; fi )
@@ -1376,16 +1350,17 @@ fi
 
 # Define the function that will be used to run a single job
 function _run() {
-  local par_wellBarcodeLength="\$1"
-  local par_UMIlength="\$2"
-  local par_output="\$3"
-  local par_genomeDir="\$4"
-  local par_limitBAMsortRAM="\$5"
-  local par_runThreadN="\$6"
-  local barcode="\$7"
-  local input_R1="\$8"
-  local input_R2="\$9"
-  local par_UMIstart=\$((\$par_wellBarcodeLength + 1))
+  local par_UMIlength="\$1"
+  local par_output="\$2"
+  local par_genomeDir="\$3"
+  local par_limitBAMsortRAM="\$4"
+  local par_runThreadN="\$5"
+  local barcode="\$6"
+  local input_R1="\$7"
+  local input_R2="\$8"
+
+  local barcode_length="\${#barcode}"
+  local umi_start="\$((\$barcode_length + 1))"
 
   set -eo pipefail
 
@@ -1481,8 +1456,8 @@ function _run() {
     --outSAMtype BAM SortedByCoordinate \\
     --soloCBstart 1 \\
     --readFilesType "Fastx" \\
-    --soloCBlen "\$par_wellBarcodeLength" \\
-    --soloUMIstart "\$par_UMIstart" \\
+    --soloCBlen "\$barcode_length" \\
+    --soloUMIstart "\$umi_start" \\
     --soloUMIlen "\$par_UMIlength" \\
     --soloBarcodeReadLength 0 \\
     --soloStrand Unstranded \\
@@ -1538,7 +1513,7 @@ parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
               "--joblog" "\$par_joblog" "_run" "{}")
 
 # Arguments for which there is one value, so these will not create extra jobs
-parallel_cmd+=(":::" "\$par_wellBarcodesLength" ":::" "\$par_umiLength" ":::" "\$par_output" ":::" "\$par_genomeDir" ":::" "\$par_limitBAMsortRAM" ":::" "\$par_runThreadN")
+parallel_cmd+=(":::" "\$par_umiLength" ":::" "\$par_output" ":::" "\$par_genomeDir" ":::" "\$par_limitBAMsortRAM" ":::" "\$par_runThreadN")
 
 # Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
 # Thus, these argument lists should have the same length.
diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml
index 71d3c333..3f145308 100644
--- a/target/executable/report/create_report/.config.vsh.yaml
+++ b/target/executable/report/create_report/.config.vsh.yaml
@@ -201,8 +201,8 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report
index e7d9cdfc..691eca5d 100755
--- 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="2025-01-10T15:09:09Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml
index 48d48734..293d3ef4 100644
--- a/target/executable/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml
@@ -198,8 +198,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs
index 8bae2f24..f3bfe9cc 100755
--- 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="2025-01-10T15:09:09Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
index 6d6affad..bf44bd8c 100644
--- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml
@@ -182,8 +182,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics
index e7ec677a..59482a83 100755
--- 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="2025-01-10T15:09:08Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
index 11a00386..933c35c7 100644
--- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml
@@ -262,8 +262,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics
index 2401c8bd..441b45ed 100755
--- 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="2025-01-10T15:09:09Z"
+LABEL org.opencontainers.image.created="2025-01-14T07:38:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
+LABEL org.opencontainers.image.revision="d8c0c0f518e9359c5373ff2761a80050ebb7333e"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER
diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml
index 5b6c0cf3..e9198b44 100644
--- a/target/nextflow/eset/create_eset/.config.vsh.yaml
+++ b/target/nextflow/eset/create_eset/.config.vsh.yaml
@@ -170,44 +170,22 @@ runners:
 engines:
 - type: "docker"
   id: "docker"
-  image: "r-base:4.3.0"
+  image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
   target_tag: "main"
   namespace_separator: "/"
   setup:
-  - type: "apt"
-    packages:
-    - "libcurl4-openssl-dev"
-    - "libssl-dev"
-    - "libxml2-dev"
-    - "libfftw3-dev"
-    - "libfontconfig1-dev"
-    - "libfreetype-dev"
-    - "libhdf5-dev"
-    - "bzip2"
-    - "libharfbuzz-dev"
-    - "libfribidi-dev"
-    - "libtiff-dev"
-    - "libgsl-dev"
-    - "libcairo-dev"
-    - "libudunits2-dev"
-    - "procps"
-    interactive: false
   - type: "r"
     cran:
+    - "data.table"
     - "nlcv"
     bioc:
-    - "Biobase"
-    - "limma"
-    - "a4Core"
-    - "MLInterfaces"
-    - "multtest"
-    script:
-    - "remotes::install_url(\"https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz\"\
-      , dependencies=TRUE, upgrade_dependencies=FALSE);\\\nremotes::install_url(\"\
-      https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz\"\
-      , repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\\\
-      \n"
+    - "Seurat"
+    bioc_force_install: false
+  test_setup:
+  - type: "r"
+    cran:
+    - "testthat"
     bioc_force_install: false
   entrypoint: []
   cmd: null
@@ -220,8 +198,8 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf
index 1ff6e822..6f9f488b 100644
--- a/target/nextflow/eset/create_eset/main.nf
+++ b/target/nextflow/eset/create_eset/main.nf
@@ -3034,46 +3034,28 @@ meta = [
     {
       "type" : "docker",
       "id" : "docker",
-      "image" : "r-base:4.3.0",
+      "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
       "target_tag" : "main",
       "namespace_separator" : "/",
       "setup" : [
-        {
-          "type" : "apt",
-          "packages" : [
-            "libcurl4-openssl-dev",
-            "libssl-dev",
-            "libxml2-dev",
-            "libfftw3-dev",
-            "libfontconfig1-dev",
-            "libfreetype-dev",
-            "libhdf5-dev",
-            "bzip2",
-            "libharfbuzz-dev",
-            "libfribidi-dev",
-            "libtiff-dev",
-            "libgsl-dev",
-            "libcairo-dev",
-            "libudunits2-dev",
-            "procps"
-          ],
-          "interactive" : false
-        },
         {
           "type" : "r",
           "cran" : [
+            "data.table",
             "nlcv"
           ],
           "bioc" : [
-            "Biobase",
-            "limma",
-            "a4Core",
-            "MLInterfaces",
-            "multtest"
+            "Seurat"
           ],
-          "script" : [
-            "remotes::install_url(\\"https://cran.r-project.org/src/contrib/Archive/Matrix/Matrix_1.6-5.tar.gz\\", dependencies=TRUE, upgrade_dependencies=FALSE);\\\\\nremotes::install_url(\\"https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.4.0.tar.gz\\", repos=BiocManager::repositories(), dependencies=TRUE, upgrade_dependencies=FALSE)\\\\\n"
+          "bioc_force_install" : false
+        }
+      ],
+      "test_setup" : [
+        {
+          "type" : "r",
+          "cran" : [
+            "testthat"
           ],
           "bioc_force_install" : false
         }
@@ -3090,8 +3072,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3391,7 +3373,7 @@ create_exprs_matrix <- function(exprs_matrix_path, exprs_file_paths,
   requireNamespace("Seurat")
   seurat_object <- Seurat::CreateSeuratObject(counts = read_matrix)
 
-  exprs_matrix <- as.matrix(seurat_object[['RNA']]@counts)
+  exprs_matrix <- as.matrix(seurat_object[['RNA']]\\$counts)
   # replace "-" with "_" for features with "_" 
   # before converting to Seurat object
   rownames(exprs_matrix)[idx] <- gsub("-", "_", rownames(exprs_matrix)[idx])
diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml
index 28138cd9..b9b51ba2 100644
--- a/target/nextflow/eset/create_fdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml
@@ -177,8 +177,8 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf
index bb0c78d9..3f1130ee 100644
--- a/target/nextflow/eset/create_fdata/main.nf
+++ b/target/nextflow/eset/create_fdata/main.nf
@@ -3044,8 +3044,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml
index f9409993..9548c236 100644
--- a/target/nextflow/eset/create_pdata/.config.vsh.yaml
+++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml
@@ -191,8 +191,8 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf
index a29d55cf..e075d90f 100644
--- a/target/nextflow/eset/create_pdata/main.nf
+++ b/target/nextflow/eset/create_pdata/main.nf
@@ -3058,8 +3058,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
index 7f4a6bb0..f2ca7050 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml
@@ -148,8 +148,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
index b4960b10..ff93d80f 100644
--- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
+++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf
@@ -2997,8 +2997,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git 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
index ceec13a6..8f4f7c7f 100644
--- 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
@@ -158,8 +158,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git 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
index 413a8d67..3db002d9 100644
--- 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
@@ -3009,8 +3009,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml
index 8293c32c..261fe397 100644
--- a/target/nextflow/parallel_map/.config.vsh.yaml
+++ b/target/nextflow/parallel_map/.config.vsh.yaml
@@ -68,14 +68,6 @@ argument_groups:
     multiple_sep: ";"
 - name: "Barcode arguments"
   arguments:
-  - type: "integer"
-    name: "--wellBarcodesLength"
-    description: "The length of the well barcodes"
-    info: null
-    required: true
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
   - type: "integer"
     name: "--umiLength"
     description: "The length of the UMIs"
@@ -264,8 +256,8 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf
index eb0ba085..6d68a701 100644
--- a/target/nextflow/parallel_map/main.nf
+++ b/target/nextflow/parallel_map/main.nf
@@ -2903,15 +2903,6 @@ meta = [
     {
       "name" : "Barcode arguments",
       "arguments" : [
-        {
-          "type" : "integer",
-          "name" : "--wellBarcodesLength",
-          "description" : "The length of the well barcodes",
-          "required" : true,
-          "direction" : "input",
-          "multiple" : false,
-          "multiple_sep" : ";"
-        },
         {
           "type" : "integer",
           "name" : "--umiLength",
@@ -3148,8 +3139,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3207,7 +3198,6 @@ $( if [ ! -z ${VIASH_PAR_INPUT_R1+x} ]; then echo "${VIASH_PAR_INPUT_R1}" | sed
 $( if [ ! -z ${VIASH_PAR_INPUT_R2+x} ]; then echo "${VIASH_PAR_INPUT_R2}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_r2='&'#" ; else echo "# par_input_r2="; fi )
 $( if [ ! -z ${VIASH_PAR_GENOMEDIR+x} ]; then echo "${VIASH_PAR_GENOMEDIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_genomeDir='&'#" ; else echo "# par_genomeDir="; fi )
 $( if [ ! -z ${VIASH_PAR_BARCODES+x} ]; then echo "${VIASH_PAR_BARCODES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_barcodes='&'#" ; else echo "# par_barcodes="; fi )
-$( if [ ! -z ${VIASH_PAR_WELLBARCODESLENGTH+x} ]; then echo "${VIASH_PAR_WELLBARCODESLENGTH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_wellBarcodesLength='&'#" ; else echo "# par_wellBarcodesLength="; fi )
 $( if [ ! -z ${VIASH_PAR_UMILENGTH+x} ]; then echo "${VIASH_PAR_UMILENGTH}" | sed "s#'#'\\"'\\"'#g;s#.*#par_umiLength='&'#" ; else echo "# par_umiLength="; fi )
 $( if [ ! -z ${VIASH_PAR_LIMITBAMSORTRAM+x} ]; then echo "${VIASH_PAR_LIMITBAMSORTRAM}" | sed "s#'#'\\"'\\"'#g;s#.*#par_limitBAMsortRAM='&'#" ; else echo "# par_limitBAMsortRAM="; fi )
 $( if [ ! -z ${VIASH_PAR_RUNTHREADN+x} ]; then echo "${VIASH_PAR_RUNTHREADN}" | sed "s#'#'\\"'\\"'#g;s#.*#par_runThreadN='&'#" ; else echo "# par_runThreadN="; fi )
@@ -3294,16 +3284,17 @@ fi
 
 # Define the function that will be used to run a single job
 function _run() {
-  local par_wellBarcodeLength="\\$1"
-  local par_UMIlength="\\$2"
-  local par_output="\\$3"
-  local par_genomeDir="\\$4"
-  local par_limitBAMsortRAM="\\$5"
-  local par_runThreadN="\\$6"
-  local barcode="\\$7"
-  local input_R1="\\$8"
-  local input_R2="\\$9"
-  local par_UMIstart=\\$((\\$par_wellBarcodeLength + 1))
+  local par_UMIlength="\\$1"
+  local par_output="\\$2"
+  local par_genomeDir="\\$3"
+  local par_limitBAMsortRAM="\\$4"
+  local par_runThreadN="\\$5"
+  local barcode="\\$6"
+  local input_R1="\\$7"
+  local input_R2="\\$8"
+
+  local barcode_length="\\${#barcode}"
+  local umi_start="\\$((\\$barcode_length + 1))"
 
   set -eo pipefail
 
@@ -3399,8 +3390,8 @@ function _run() {
     --outSAMtype BAM SortedByCoordinate \\\\
     --soloCBstart 1 \\\\
     --readFilesType "Fastx" \\\\
-    --soloCBlen "\\$par_wellBarcodeLength" \\\\
-    --soloUMIstart "\\$par_UMIstart" \\\\
+    --soloCBlen "\\$barcode_length" \\\\
+    --soloUMIstart "\\$umi_start" \\\\
     --soloUMIlen "\\$par_UMIlength" \\\\
     --soloBarcodeReadLength 0 \\\\
     --soloStrand Unstranded \\\\
@@ -3456,7 +3447,7 @@ parallel_cmd=("parallel" "--jobs" "80%" "--verbose" "--memfree" "2G"
               "--joblog" "\\$par_joblog" "_run" "{}")
 
 # Arguments for which there is one value, so these will not create extra jobs
-parallel_cmd+=(":::" "\\$par_wellBarcodesLength" ":::" "\\$par_umiLength" ":::" "\\$par_output" ":::" "\\$par_genomeDir" ":::" "\\$par_limitBAMsortRAM" ":::" "\\$par_runThreadN")
+parallel_cmd+=(":::" "\\$par_umiLength" ":::" "\\$par_output" ":::" "\\$par_genomeDir" ":::" "\\$par_limitBAMsortRAM" ":::" "\\$par_runThreadN")
 
 # Argument which in fact will cause extra jobs to be spawned, per job one item from each argument will be selected
 # Thus, these argument lists should have the same length.
diff --git a/target/nextflow/parallel_map/nextflow_schema.json b/target/nextflow/parallel_map/nextflow_schema.json
index 98abd686..f5cf6457 100644
--- a/target/nextflow/parallel_map/nextflow_schema.json
+++ b/target/nextflow/parallel_map/nextflow_schema.json
@@ -64,16 +64,6 @@
     "properties": {
     
         
-                "wellBarcodesLength": {
-                "type":
-                "integer",
-                "description": "Type: `integer`, required. The length of the well barcodes",
-                "help_text": "Type: `integer`, required. The length of the well barcodes"
-            
-            }
-    
-
-        ,
                 "umiLength": {
                 "type":
                 "integer",
diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml
index 0ad4955e..fe57a23c 100644
--- a/target/nextflow/report/create_report/.config.vsh.yaml
+++ b/target/nextflow/report/create_report/.config.vsh.yaml
@@ -201,8 +201,8 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf
index 1e3975b9..cb1e6c17 100644
--- a/target/nextflow/report/create_report/main.nf
+++ b/target/nextflow/report/create_report/main.nf
@@ -3077,8 +3077,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
index f6d9ee2d..5c75de3f 100644
--- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
+++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml
@@ -198,8 +198,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf
index 0ab46987..348319ba 100644
--- a/target/nextflow/stats/combine_star_logs/main.nf
+++ b/target/nextflow/stats/combine_star_logs/main.nf
@@ -3060,8 +3060,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
index 2104c015..a69a415e 100644
--- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml
@@ -182,8 +182,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf
index 26fec4ec..3ffedf28 100644
--- a/target/nextflow/stats/generate_pool_statistics/main.nf
+++ b/target/nextflow/stats/generate_pool_statistics/main.nf
@@ -3044,8 +3044,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
index 776e27c3..4bb2e4d3 100644
--- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
+++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml
@@ -262,8 +262,8 @@ 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: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf
index 48735434..e3a01819 100644
--- a/target/nextflow/stats/generate_well_statistics/main.nf
+++ b/target/nextflow/stats/generate_well_statistics/main.nf
@@ -3135,8 +3135,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
index 3ca2b258..0c7c1f0d 100644
--- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
+++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml
@@ -51,6 +51,17 @@ argument_groups:
     direction: "input"
     multiple: false
     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: ";"
   - type: "file"
     name: "--genomeDir"
     info: null
@@ -308,8 +319,8 @@ build_info:
   output: "target/nextflow/workflows/htrnaseq"
   executable: "target/nextflow/workflows/htrnaseq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/stats/combine_star_logs"
   - "target/nextflow/stats/generate_pool_statistics"
diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf
index 62d60ded..25421e31 100644
--- a/target/nextflow/workflows/htrnaseq/main.nf
+++ b/target/nextflow/workflows/htrnaseq/main.nf
@@ -2869,6 +2869,19 @@ meta = [
           "multiple" : false,
           "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" : ";"
+        },
         {
           "type" : "file",
           "name" : "--genomeDir",
@@ -3210,8 +3223,8 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/htrnaseq",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3306,6 +3319,7 @@ workflow run_wf {
             "input_r1": state.fastq_output_r1[0],
             "input_r2": state.fastq_output_r2[0],
             "barcode": state.barcode,
+            "umi_length": state.umi_length,
             "pool": state.pool,
             "output": state.star_output[0],
             "genomeDir": state.genomeDir,
diff --git a/target/nextflow/workflows/htrnaseq/nextflow_schema.json b/target/nextflow/workflows/htrnaseq/nextflow_schema.json
index 6ce186b6..6d91f673 100644
--- a/target/nextflow/workflows/htrnaseq/nextflow_schema.json
+++ b/target/nextflow/workflows/htrnaseq/nextflow_schema.json
@@ -43,6 +43,17 @@
             }
     
 
+        ,
+                "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
+            }
+    
+
         ,
                 "genomeDir": {
                 "type":
diff --git a/target/nextflow/workflows/parallel_map_wf/.config.vsh.yaml b/target/nextflow/workflows/parallel_map_wf/.config.vsh.yaml
index f7d56e6c..79280fb7 100644
--- a/target/nextflow/workflows/parallel_map_wf/.config.vsh.yaml
+++ b/target/nextflow/workflows/parallel_map_wf/.config.vsh.yaml
@@ -43,6 +43,14 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
+  - type: "integer"
+    name: "--umi_length"
+    info: null
+    required: false
+    min: 1
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
   - type: "string"
     name: "--pool"
     info: null
@@ -175,8 +183,8 @@ build_info:
   output: "target/nextflow/workflows/parallel_map_wf"
   executable: "target/nextflow/workflows/parallel_map_wf/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/nextflow/parallel_map"
   - "target/nextflow/workflows/utils/groupWells"
diff --git a/target/nextflow/workflows/parallel_map_wf/main.nf b/target/nextflow/workflows/parallel_map_wf/main.nf
index b066ec8e..051791da 100644
--- a/target/nextflow/workflows/parallel_map_wf/main.nf
+++ b/target/nextflow/workflows/parallel_map_wf/main.nf
@@ -2865,6 +2865,15 @@ meta = [
           "multiple" : false,
           "multiple_sep" : ";"
         },
+        {
+          "type" : "integer",
+          "name" : "--umi_length",
+          "required" : false,
+          "min" : 1,
+          "direction" : "input",
+          "multiple" : false,
+          "multiple_sep" : ";"
+        },
         {
           "type" : "string",
           "name" : "--pool",
@@ -3028,8 +3037,8 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/parallel_map_wf",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
@@ -3104,8 +3113,7 @@ workflow run_wf {
            "genomeDir": state.genomeDir,
            "barcodes": state.wells,
            "pool": state.pool,
-           "wellBarcodesLength": 10,
-           "umiLength": 10,
+           "umiLength": state.umi_length,
            "output": state.output,
          ]
         },
diff --git a/target/nextflow/workflows/parallel_map_wf/nextflow_schema.json b/target/nextflow/workflows/parallel_map_wf/nextflow_schema.json
index 7585ff9a..d897ee21 100644
--- a/target/nextflow/workflows/parallel_map_wf/nextflow_schema.json
+++ b/target/nextflow/workflows/parallel_map_wf/nextflow_schema.json
@@ -43,6 +43,16 @@
             }
     
 
+        ,
+                "umi_length": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. ",
+                "help_text": "Type: `integer`. "
+            
+            }
+    
+
         ,
                 "pool": {
                 "type":
diff --git a/target/nextflow/workflows/utils/groupWells/.config.vsh.yaml b/target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
index afec17e8..e10c326b 100644
--- a/target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
+++ b/target/nextflow/workflows/utils/groupWells/.config.vsh.yaml
@@ -185,8 +185,8 @@ build_info:
   output: "target/nextflow/workflows/utils/groupWells"
   executable: "target/nextflow/workflows/utils/groupWells/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
 package_config:
   name: "htrnaseq"
   version: "main"
diff --git a/target/nextflow/workflows/utils/groupWells/main.nf b/target/nextflow/workflows/utils/groupWells/main.nf
index 63069778..032b5768 100644
--- a/target/nextflow/workflows/utils/groupWells/main.nf
+++ b/target/nextflow/workflows/utils/groupWells/main.nf
@@ -3039,8 +3039,8 @@ meta = [
     "engine" : "native",
     "output" : "target/nextflow/workflows/utils/groupWells",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",
diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
index b45a699f..0d460f81 100644
--- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
+++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml
@@ -255,8 +255,8 @@ build_info:
   output: "target/nextflow/workflows/well_demultiplex"
   executable: "target/nextflow/workflows/well_demultiplex/main.nf"
   viash_version: "0.9.0"
-  git_commit: "4a6fc3588e66c0d41a0dc31fec56ec47cb871956"
-  git_remote: "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+  git_commit: "d8c0c0f518e9359c5373ff2761a80050ebb7333e"
+  git_remote: "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt"
   - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text"
diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf
index cbd62d5c..4c5fba08 100644
--- a/target/nextflow/workflows/well_demultiplex/main.nf
+++ b/target/nextflow/workflows/well_demultiplex/main.nf
@@ -3134,8 +3134,8 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/workflows/well_demultiplex",
     "viash_version" : "0.9.0",
-    "git_commit" : "4a6fc3588e66c0d41a0dc31fec56ec47cb871956",
-    "git_remote" : "https://x-access-token:ghs_SaYCQ0uYvqLIVXUBCVNZPcP9pTStxd0Bbljy@github.com/viash-hub/htrnaseq"
+    "git_commit" : "d8c0c0f518e9359c5373ff2761a80050ebb7333e",
+    "git_remote" : "https://x-access-token:ghs_WwvhrfwIl9DJdsjBAWPXvIvgBFDL7344Rs7f@github.com/viash-hub/htrnaseq"
   },
   "package_config" : {
     "name" : "htrnaseq",